1
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Wang T, Yamato T, Sugiura W. Thermal Energy Transport through Nonbonded Native Contacts in Protein. J Phys Chem B 2024; 128:8641-8650. [PMID: 39197018 DOI: 10.1021/acs.jpcb.4c03475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.
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Affiliation(s)
- Tingting Wang
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Wataru Sugiura
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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2
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Ferreira de Souza N, Picard C, Franco LFM, Coasne B. Thermal Conductivity of a Fluid-Filled Nanoporous Material: Underlying Molecular Mechanisms and the Rattle Effect. J Phys Chem B 2024. [PMID: 38438957 DOI: 10.1021/acs.jpcb.3c07088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Nanoporous materials are central to the energy and environmental crisis, with key applications in adsorption, separation, and catalysis. While confinement and surface effects on fluids severely confined in their porosity are well documented, the thermal behavior of nanoporous solids subjected to fluid adsorption remains puzzling in many aspects. With striking phenomena such as the so-called rattle effect, through which fluid/solid collisions decrease the overall thermal conductivity, the solid thermal conductivity and, more generally, heat transfer and dispersion in these complex systems challenge classical approaches (e.g., mixing rules including effective medium approaches fail to capture such effects as shown here). In particular, a robust molecular framework to describe the crossover between the decrease in thermal conductivity through the rattle effect in very narrow pores and the increase in thermal conductivity when replacing vacuum with a fluid phase in larger pores is still missing. Here, using a prototypical model of fluid-filled nanoporous materials (a Lennard-Jones phase confined in an all-silica zeolite), we perform a molecular simulation study to shed light on the parameters that govern the rattle effect in nanoporous solids. First, by varying the fluid/fluid, fluid/solid, and solid/solid interaction strengths as well as the fluid number density and mass density, we unravel the ingredients that lead to the essential coupling between fluid adsorption and phonon transport. Second, despite this complex interplay, inspired by pioneering molecular approaches on the rattle effect, we show that all data obey a simple statistical physics model that relies on the change in the speed of sound due to the fluid adsorbed density and the decrease in phonon lifetime due to scattering by fluid molecules. This framework, which provides a simple formalism to rationalize the thermal behavior of this class of solid/fluid composites, points to a decrease in thermal conductivity upon fluid confinement (up to 30% in some cases). Such an effect paves the way for the design of novel applications involving fluids in interaction with nanoporous materials.
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Affiliation(s)
- Nikolas Ferreira de Souza
- School of Chemical Engineering, Department of Chemical Systems Engineering, University of Campinas, 13083-852 Campinas, Brazil
- University Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Cyril Picard
- University Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Luís Fernando Mercier Franco
- School of Chemical Engineering, Department of Chemical Systems Engineering, University of Campinas, 13083-852 Campinas, Brazil
| | - Benoit Coasne
- University Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
- Institut Laue-Langevin, F-38042 Grenoble, France
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3
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Lucia U, Fino D, Deisboeck TS, Grisolia G. A Thermodynamic Perspective of Cancer Cells' Volume/Area Expansion Ratio. MEMBRANES 2023; 13:895. [PMID: 38132898 PMCID: PMC10744848 DOI: 10.3390/membranes13120895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
The constructal law is used to improve the analysis of the resonant heat transfer in cancer cells. The result highlights the fundamental role of the volume/area ratio and its role in cancer growth and invasion. Cancer cells seek to increase their surface area to facilitate heat dissipation; as such, the tumour expansion ratio declines as malignant cells start to migrate and the cancer expands locally and systemically. Consequently, we deduce that effective anticancer therapy should be based on the control of some ion transport phenomena in an effort to increase the volume/area ratio. This emphasises restricting the local and systemic spatial expansion of the tumour system and thus gives further credence to the superior role of novel anti-migratory and anti-invasive treatment strategies over conventional anti-proliferative options only.
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Affiliation(s)
- Umberto Lucia
- Dipartimento Energia “Galileo Ferraris”, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Debora Fino
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Thomas S. Deisboeck
- Department of Radiology, Harvard-MIT Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, MA 02129, USA
| | - Giulia Grisolia
- Dipartimento di Ingegneria dell’Ambiente, del Territorio e delle Infrastrutture, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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4
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Rabani R, Saidi MH, Rajabpour A, Joly L, Merabia S. Enhanced Heat Flow between Charged Nanoparticles and an Aqueous Electrolyte. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15222-15230. [PMID: 37865920 DOI: 10.1021/acs.langmuir.3c01847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Heat transfer through the interface between a metallic nanoparticle and an electrolyte solution has great importance in a number of applications, ranging from nanoparticle-based cancer treatments to nanofluids and solar energy conversion devices. However, the impact of the surface charge and dissolved ions on heat transfer has been scarcely explored so far. In this study, we compute the interface thermal conductance between hydrophilic and hydrophobic charged gold nanoparticles immersed in an electrolyte using equilibrium molecular dynamics simulations. Compared with an uncharged nanoparticle, we report a 3-fold increase of the Kapitza conductance for a nanoparticle surface charge of +320 mC/m2. This enhancement is shown to be approximately independent of the surface wettability, charge spatial distribution, and salt concentration. This allows us to express the Kapitza conductance enhancement in terms of the surface charge density on a master curve. Finally, we interpret the increase of the Kapitza conductance as a combined result of the shift of the water density distribution toward the charged nanoparticle and an accumulation of the counterions around the nanoparticle surface which increase the Coulombic interaction between the liquid and the charged nanoparticle. These considerations help us to apprehend the role of ions in heat transfer close to electrified surfaces.
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Affiliation(s)
- Reza Rabani
- Department of Mechanical Engineering, Karaj Branch, Islamic Azad University, Karaj 31499-68111, Iran
| | - Mohammad Hassan Saidi
- Center of Excellence in Energy Conversion (CEEC), School of Mechanical Engineering, Sharif University of Technology, Tehran 11155-9567, Iran
| | - Ali Rajabpour
- Advanced Simulation and Computing Laboratory (ASCL), Mechanical Engineering Department, Imam Khomeini International University, Qazvin 34148-96818, Iran
| | - Laurent Joly
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Samy Merabia
- Institut Lumière Matière, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
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5
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Samolis PD, Sander MY, Hong MK, Erramilli S, Narayan O. Thermal transport across membranes and the Kapitza length from photothermal microscopy. J Biol Phys 2023; 49:365-381. [PMID: 37477759 PMCID: PMC10397174 DOI: 10.1007/s10867-023-09636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/30/2023] [Indexed: 07/22/2023] Open
Abstract
An analytical model is presented for light scattering associated with heat transport near a cell membrane that divides a complex system into two topologically distinct half-spaces. Our analysis is motivated by experiments on vibrational photothermal microscopy which have not only demonstrated remarkably high contrast and resolution, but also are capable of providing label-free local information of heat transport in complex morphologies. In the first Born approximation, the derived Green's function leads to the reconstruction of a full 3D image with photothermal contrast obtained using both amplitude and phase detection of periodic excitations. We show that important fundamental parameters including the Kapitza length and Kapitza resistance can be derived from experiments. Our goal is to spur additional experimental studies with high-frequency modulation and heterodyne detection in order to make contact with recent theoretical molecular dynamics calculations of thermal transport properties in membrane systems.
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Affiliation(s)
- Panagis D Samolis
- Department of Electrical Engineering, Boston University, Boston, MA, 02215, USA
- The Photonics Center, Boston University, Boston, MA, 02215, USA
| | - Michelle Y Sander
- Department of Electrical Engineering, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- The Photonics Center, Boston University, Boston, MA, 02215, USA
| | - Mi K Hong
- Department of Physics, Boston University, Boston, MA, 02215, USA
| | - Shyamsunder Erramilli
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- The Photonics Center, Boston University, Boston, MA, 02215, USA.
- Department of Physics, Boston University, Boston, MA, 02215, USA.
| | - Onuttom Narayan
- Department of Physics, University of California Santa Cruz, Santa Cruz, CA, USA.
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6
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Saurabh S, Li Z, Hollowell P, Waigh T, Li P, Webster J, Seddon JM, Kalonia C, Lu JR, Bresme F. Structure and interaction of therapeutic proteins in solution: a combined simulation and experimental study. Mol Phys 2023; 121:e2236248. [PMID: 38107421 PMCID: PMC10721229 DOI: 10.1080/00268976.2023.2236248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 12/19/2023]
Abstract
The aggregation of therapeutic proteins in solution has attracted significant interest, driving efforts to understand the relationship between microscopic structural changes and protein-protein interactions determining aggregation processes in solution. Additionally, there is substantial interest in being able to predict aggregation based on protein structure as part of molecular developability assessments. Molecular Dynamics provides theoretical tools to complement experimental studies and to interrogate and identify the microscopic mechanisms determining aggregation. Here we perform all-atom MD simulations to study the structure and inter-protein interaction of the Fab and Fc fragments of the monoclonal antibody (mAb) COE3. We unravel the role of ion-protein interactions in building the ionic double layer and determining effective inter-protein interaction. Further, we demonstrate, using various state-of-the-art force fields (charmm, gromos, amber, opls/aa), that the protein solvation, ionic structure and protein-protein interaction depend significantly on the force field parameters. We perform SANS and Static Light Scattering experiments to assess the accuracy of the different forcefields. Comparison of the simulated and experimental results reveal significant differences in the forcefields' performance, particularly in their ability to predict the protein size in solution and inter-protein interactions quantified through the second virial coefficients. In addition, the performance of the forcefields is correlated with the protein hydration structure.
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Affiliation(s)
- Suman Saurabh
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
| | - Zongyi Li
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Peter Hollowell
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Thomas Waigh
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
- Photon Science Institute, The University of Manchester, Manchester, UK
| | - Peixun Li
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot, UK
| | - John Webster
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot, UK
| | - John M. Seddon
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
| | - Cavan Kalonia
- Dosage Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jian R. Lu
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
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7
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Wazawa T, Nagai T. Joule heating involving ion currents through channel proteins. Biophys Physicobiol 2023; 20:e200030. [PMID: 38124793 PMCID: PMC10728626 DOI: 10.2142/biophysico.bppb-v20.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/26/2023] [Indexed: 12/23/2023] Open
Abstract
Ion currents associated with channel proteins in the presence of membrane potential are ubiquitous in cellular and organelle membranes. When an ion current occurs through a channel protein, Joule heating should occur. However, this Joule heating seems to have been largely overlooked in biology. Here we show theoretical investigation of Joule heating involving channel proteins in biological processes. We used electrochemical potential to derive the Joule's law for an ion current through an ion transport protein in the presence of membrane potential, and we suggest that heat production and absorption can occur. Simulation of temperature distribution around a single channel protein with the Joule heating revealed that the temperature increase was as small as <10-3 K, although an ensemble of channel proteins was suggested to exhibit a noticeable temperature increase. Thereby, we theoretically investigated the Joule heating of systems containing ensembles of channel proteins. Nerve is known to undergo rapid heat production followed by heat absorption during the action potential, and our simulation of Joule heating for a squid giant axon combined with the Hodgkin-Huxley model successfully reproduced the feature of the heat. Furthermore, we extended the theory of Joule heating to uncoupling protein 1 (UCP1), a solute carrier family transporter, which is important to the non-shivering thermogenesis in brown adipose tissue mitochondria (BATM). Our calculations showed that the Joule heat involving UCP1 was comparable to the literature calorimetry data of BATM. Joule heating of ion transport proteins is likely to be one of important mechanisms of cellular thermogenesis.
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Affiliation(s)
| | - Takeharu Nagai
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan
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8
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Kurisaki I, Tanaka S, Mori I, Umegaki T, Mori Y, Tanaka S. Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape. J Comput Chem 2023; 44:857-868. [PMID: 36468822 PMCID: PMC10107505 DOI: 10.1002/jcc.27048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/10/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
Considering the importance of elucidating the heat transfer in living cells, we evaluated the thermal conductivity κ and conductance G of hydrated protein through all-atom non-equilibrium molecular dynamics simulation. Extending the computational scheme developed in earlier studies for spherical protein to cylindrical one under the periodic boundary condition, we enabled the theoretical analysis of anisotropic thermal conduction and also discussed the effects of protein size correction on the calculated results. While the present results for myoglobin and green fluorescent protein (GFP) by the spherical model were in fair agreement with previous computational and experimental results, we found that the evaluations for κ and G by the cylindrical model, in particular, those for the longitudinal direction of GFP, were enhanced substantially, but still keeping a consistency with experimental data. We also studied the influence by salt addition of physiological concentration, finding insignificant alteration of thermal conduction of protein in the present case.
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Affiliation(s)
- Ikuo Kurisaki
- Graduate School of System Informatics, Kobe University, Kobe, Japan
| | - Seiya Tanaka
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Ichiro Mori
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Toshihito Umegaki
- Graduate School of System Informatics, Kobe University, Kobe, Japan.,Center for Mathematical Modeling and Data Science, Osaka University, Osaka, Japan
| | - Yoshiharu Mori
- Graduate School of System Informatics, Kobe University, Kobe, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, Kobe, Japan
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9
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Kurisaki I, Suzuki M. Simulation toolkits at the molecular scale for trans-scale thermal signaling. Comput Struct Biotechnol J 2023; 21:2547-2557. [PMID: 37102156 PMCID: PMC10123322 DOI: 10.1016/j.csbj.2023.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/28/2023] Open
Abstract
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.
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Affiliation(s)
- Ikuo Kurisaki
- Waseda Research Institute for Science and Engineering, Waseda University, Bldg. No.55, S Tower, 4th Floor, 3–4-1 Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Corresponding authors.
| | - Madoka Suzuki
- Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka 565–0871, Japan
- Corresponding authors.
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10
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Huang A, Chen W, Wu C, Lee T, Huang C, Kuo H. Characterization of nasal aerodynamics and air conditioning ability using CFD and its application to improve the empty nose syndrome (ENS) submucosal floor implant surgery – Part I methodology. J Taiwan Inst Chem Eng 2022. [DOI: 10.1016/j.jtice.2022.104481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Wang Z, Cheng H, Sheng Y, Chen Z, Zhu X, Ren J, Zhang X, Lv L, Zhang H, Zhou J, Ding Y. Biofunctionalized graphene oxide nanosheet for amplifying antitumor therapy: Multimodal high drug encapsulation, prolonged hyperthermal window, and deep-site burst drug release. Biomaterials 2022; 287:121629. [PMID: 35724541 DOI: 10.1016/j.biomaterials.2022.121629] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/19/2022] [Accepted: 06/08/2022] [Indexed: 11/15/2022]
Abstract
Biofunctional surface-modification surpassed critical limitation of graphene oxide (GO) in biocompatibility and drug delivery efficiency, contributing to versatile biomedical applications. Here, a protein corona-bridged GO nanoplatform with high drug loading, longstanding hyperthermia, and controllable drug release, was engineered for amplified tumor therapeutic benefits. Structurally, GO surface was installed with phenylboronic acid (PBA) layer, on which iRGD conjugated apolipoprotein A-I (iRGD-apoA-I) was coordinated via boron electron-deficiency, to form the sandwich-like GO nanosheet (iAPG). The GO camouflaging by iRGD-apoA-I corona provided multimodal high doxorubicin (DOX) loading by π-π stacking and coordination, and generated a higher photothermal transformation efficiency simultaneously. In vitro studies demonstrated that iAPG significantly improved drug penetration and internalization, then achieved tumor-targeted DOX release through near-infrared (NIR) controlled endo/lysosome disruption. Moreover, iAPG mediated site-specific drug shuttling to produce a 3.53-fold enhancement of tumor drug-accumulation compared to the free DOX in vivo, and induced deep tumor penetration dramatically. Primary tumor ablation and spontaneous metastasis inhibition were further demonstrated with negligible side effects under optimal NIR. Taken together, our work provided multifunctional protein corona strategy to inorganic nanomaterials toward advantageous biomedical applications.
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Affiliation(s)
- Zhen Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Hao Cheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Yu Sheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Zongkai Chen
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Xiaohong Zhu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Jianye Ren
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Xiangze Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Lingyu Lv
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Huaqing Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Jianping Zhou
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China.
| | - Yang Ding
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicines, NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China.
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12
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Chung CW, Stephens AD, Konno T, Ward E, Avezov E, Kaminski CF, Hassanali AA, Kaminski Schierle GS. Intracellular Aβ42 Aggregation Leads to Cellular Thermogenesis. J Am Chem Soc 2022; 144:10034-10041. [PMID: 35616634 PMCID: PMC9185738 DOI: 10.1021/jacs.2c03599] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The aggregation of
Aβ42 is a hallmark of Alzheimer’s
disease. It is still not known what the biochemical changes are inside
a cell which will eventually lead to Aβ42 aggregation. Thermogenesis
has been associated with cellular stress, the latter of which may
promote aggregation. We perform intracellular thermometry measurements
using fluorescent polymeric thermometers to show that Aβ42 aggregation
in live cells leads to an increase in cell-averaged temperatures.
This rise in temperature is mitigated upon treatment with an aggregation
inhibitor of Aβ42 and is independent of mitochondrial damage
that can otherwise lead to thermogenesis. With this, we present a
diagnostic assay which could be used to screen small-molecule inhibitors
to amyloid proteins in physiologically relevant settings. To interpret
our experimental observations and motivate the development of future
models, we perform classical molecular dynamics of model Aβ
peptides to examine the factors that hinder thermal dissipation. We
observe that this is controlled by the presence of ions in its surrounding
environment, the morphology of the amyloid peptides, and the extent
of its hydrogen-bonding interactions with water. We show that aggregation
and heat retention by Aβ peptides are favored under intracellular-mimicking
ionic conditions, which could potentially promote thermogenesis. The
latter will, in turn, trigger further nucleation events that accelerate
disease progression.
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Affiliation(s)
- Chyi Wei Chung
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Amberley D Stephens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Tasuku Konno
- UK Dementia Research Institute, Department of Clinical Neuroscience, University of Cambridge, Cambridge CB2 0AH, U.K
| | - Edward Ward
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Edward Avezov
- UK Dementia Research Institute, Department of Clinical Neuroscience, University of Cambridge, Cambridge CB2 0AH, U.K
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Ali A Hassanali
- Condensed Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
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13
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Yamato T, Wang T, Sugiura W, Laprévote O, Katagiri T. Computational Study on the Thermal Conductivity of a Protein. J Phys Chem B 2022; 126:3029-3036. [PMID: 35416670 DOI: 10.1021/acs.jpcb.2c00958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein molecules are thermally fluctuating and tightly packed amino acid residues strongly interact with each other. Such interactions are characterized in terms of heat current at the atomic level. We calculated the thermal conductivity of a small globular protein, villin headpiece subdomain, based on the linear response theory using equilibrium molecular dynamics simulation. The value of its thermal conductivity was 0.3 ± 0.01 [W m-1 K-1], which is in good agreement with experimental and computational studies on the other proteins in the literature. Heat current along the main chain was dominated by local vibrations in the polypeptide bonds, with amide I, II, III, and A bands on the Fourier transform of the heat current autocorrelation function.
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Affiliation(s)
- Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tingting Wang
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Wataru Sugiura
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Olivier Laprévote
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takahiro Katagiri
- Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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14
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Jiang M, Olarte-Plata JD, Bresme F. Heterogeneous thermal conductance of nanoparticle–fluid interfaces: An atomistic nodal approach. J Chem Phys 2022; 156:044701. [DOI: 10.1063/5.0074912] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Mingxuan Jiang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Juan D. Olarte-Plata
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
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15
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Hamzi H, Rajabpour A, Roldán É, Hassanali A. Learning the Hydrophobic, Hydrophilic, and Aromatic Character of Amino Acids from Thermal Relaxation and Interfacial Thermal Conductance. J Phys Chem B 2022; 126:670-678. [PMID: 35015542 DOI: 10.1021/acs.jpcb.1c07628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, the thermal relaxation of the 20 naturally occurring amino acids in water and in the protein lysozyme is investigated using transient nonequilibrium molecular dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the amino acids in water occurs over a time scale covering 2-5 ps. For the hydrophobic amino acids, the relaxation time is controlled by the size of the hydrocarbon side chain, while for hydrophilic amino acids, the number of hydrogen bonds does not significantly affect the time scales of the heat dissipation. Our results show that the interfacial thermal conductance at the amino acid-water interface is in the range of 40-80 MW m-2 K-1. Hydrophobic and aromatic amino acids tend to have a lower interfacial thermal conductance. Notably, we show that amino acids can be correlated with their thermal relaxation times and molar masses, into simply connected phases with the same hydrophilicity, hydrophobicity, and aromaticity. The thermal relaxation slows down by a factor of up to five in the protein relative to that in water. In the case of the hydrophobic amino acids in the protein lysozyme, the slow down in the thermal relaxation relative to that in water appears to be controlled primarily by the size of the side chain.
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Affiliation(s)
- Heydar Hamzi
- Advanced Simulation and Computing Laboratory (ASCL), Mechanical Engineering Department, Imam Khomeini International University, Qazvin 34148-96818, Iran
| | - Ali Rajabpour
- Advanced Simulation and Computing Laboratory (ASCL), Mechanical Engineering Department, Imam Khomeini International University, Qazvin 34148-96818, Iran
| | - Édgar Roldán
- The Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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16
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Maciel GS. Pushing the limits of luminescence thermometry: probing the temperature of proteins in cells. J Biol Phys 2022; 48:167-175. [PMID: 34997472 DOI: 10.1007/s10867-021-09600-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022] Open
Abstract
Proteins are involved in numerous cellular activities such as transport and catalysis. Misfolding during biosynthesis and malfunctioning as a molecular machine may lead to physiological disorders and metabolic problems. Protein folding and mechanical work may be viewed as thermodynamic energetically favorable processes in which stochastic nonequilibrium intermediate states may be present with conditions such as thermal fluctuations. In my opinion, measuring those thermal fluctuations may be a way to access the energy exchange between the protein and the physiological environment and to better understand how those nonequilibrium states may influence the misfolding/folding process and the efficiency of the molecular engine cycle. Here, I discuss luminescence thermometry as a possible way to measure those temperature fluctuations from a single-molecule experimental perspective with its current technical limitations and challenges.
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Affiliation(s)
- Glauco S Maciel
- Instituto de Física, Universidade Federal Fluminense, Niterói, RJ, 24210-346, Brazil.
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17
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Rajagopal MC, Sinha S. Cellular Thermometry Considerations for Probing Biochemical Pathways. Cell Biochem Biophys 2021; 79:359-373. [PMID: 33797706 DOI: 10.1007/s12013-021-00979-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 12/28/2022]
Abstract
Temperature is a fundamental thermodynamic property that can serve as a probe of biochemical reactions. Extracellular thermometry has previously been used to probe cancer metabolism and thermoregulation, with measured temperature changes of ~1-2 K in tissues, consistent with theoretical predictions. In contrast, previous intracellular thermometry studies remain disputed due to reports of >1 K intracellular temperature rises over 5 min or more that are inconsistent with theory. Thus, the origins of such anomalous temperature rises remain unclear. An improved quantitative understanding of intracellular thermometry is necessary to provide a clearer perspective for future measurements. Here, we develop a generalizable framework for modeling cellular heat diffusion over a range of subcellular-to-tissue length scales. Our model shows that local intracellular temperature changes reach measurable limits (>0.1 K) only when exogenously stimulated. On the other hand, extracellular temperatures can be measurable (>0.1 K) in tissues even from endogenous biochemical pathways. Using these insights, we provide a comprehensive approach to choosing an appropriate cellular thermometry technique by analyzing thermogenic reactions of different heat rates and time constants across length scales ranging from subcellular to tissues. Our work provides clarity on cellular heat diffusion modeling and on the required thermometry approach for probing thermogenic biochemical pathways.
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Affiliation(s)
- Manjunath C Rajagopal
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sanjiv Sinha
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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18
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Samolis PD, Langley D, O’Reilly BM, Oo Z, Hilzenrat G, Erramilli S, Sgro AE, McArthur S, Sander MY. Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals. BIOMEDICAL OPTICS EXPRESS 2021; 12:303-319. [PMID: 33520386 PMCID: PMC7818956 DOI: 10.1364/boe.411888] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 05/19/2023]
Abstract
Label-free vibrational imaging of biological samples has attracted significant interest due to its integration of structural and chemical information. Vibrational infrared photothermal amplitude and phase signal (VIPPS) imaging provide label-free chemical identification by targeting the characteristic resonances of biological compounds that are present in the mid-infrared fingerprint region (3 µm - 12 µm). High contrast imaging of subcellular features and chemical identification of protein secondary structures in unlabeled and labeled fibroblast cells embedded in a collagen-rich extracellular matrix is demonstrated by combining contrast from absorption signatures (amplitude signals) with sensitive detection of different heat properties (lock-in phase signals). We present that the detectability of nano-sized cell membranes is enhanced to well below the optical diffraction limit since the membranes are found to act as thermal barriers. VIPPS offers a novel combination of chemical imaging and thermal diffusion characterization that paves the way towards label-free imaging of cell models and tissues as well as the study of intracellular heat dynamics.
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Affiliation(s)
- Panagis D. Samolis
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Daniel Langley
- Bioengineering Research Group Engineering and Technology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, CSIRO Manufacturing, Melbourne, VIC, Australia
| | - Breanna M. O’Reilly
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Zay Oo
- Bioengineering Research Group Engineering and Technology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, CSIRO Manufacturing, Melbourne, VIC, Australia
| | - Geva Hilzenrat
- Bioengineering Research Group Engineering and Technology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, CSIRO Manufacturing, Melbourne, VIC, Australia
| | - Shyamsunder Erramilli
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Physics, Boston University, Boston, MA 02215, USA
- Division of Materials Science and Engineering, Boston University, Brookline, MA 02446, USA
| | - Allyson E. Sgro
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Physics, Boston University, Boston, MA 02215, USA
| | - Sally McArthur
- Bioengineering Research Group Engineering and Technology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
- Biomedical Manufacturing, CSIRO Manufacturing, Melbourne, VIC, Australia
| | - Michelle Y. Sander
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Division of Materials Science and Engineering, Boston University, Brookline, MA 02446, USA
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19
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Ebrahimi Viand R, Höfling F, Klein R, Delle Site L. Theory and simulation of open systems out of equilibrium. J Chem Phys 2020; 153:101102. [PMID: 32933284 DOI: 10.1063/5.0014065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations.
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Affiliation(s)
- R Ebrahimi Viand
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - F Höfling
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - R Klein
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - L Delle Site
- Freie Universität Berlin, Institute of Mathematics, Arnimallee 6, 14195 Berlin, Germany
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20
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Tanaka S, Shimamura K. Temperature relaxation in binary hard-sphere mixture system: Molecular dynamics and kinetic theory study. J Chem Phys 2020; 153:034114. [PMID: 32716157 DOI: 10.1063/5.0011181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational schemes to describe the temperature relaxation in the binary hard-sphere mixture system are given on the basis of molecular dynamics (MD) simulation and renormalized kinetic theory. Event-driven MD simulations are carried out for three model systems in which the initial temperatures and the ratios of diameter and mass of two components are different to study the temporal evolution of each component temperature in nanoscale molecular conditions mimicking those in living cells. On the other hand, the temperature changes of the two components are also described in terms of a mean-field kinetic theory with the correlation functions calculated in the Percus-Yevick approximation. The calculated results by both the computational approaches have shown fair agreement with each other, whereas slight deviations have been found in the temporal range of femto- to picoseconds when the initial temperatures of the two components are significantly different, such as 300 K vs 1000 K. This discrepancy can be ascribed to the fast intra-component temperature relaxation assumed in the kinetic theory, and its violation in the MD simulations can be evaluated in terms of the Kullback-Leibler divergence between the equilibrated Maxwell-Boltzmann distribution at each temperature and the actual non-equilibrium velocity distribution realized in the MD. Thus, the present analysis provides a quantitative basis for addressing the temperature inhomogeneities experimentally observed in nanoscale crowding conditions.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, Kobe 657-8501, Japan
| | - Kohei Shimamura
- Department of Physics, Kumamoto University, Kumamoto 860-8555, Japan
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21
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Suzuki M, Plakhotnik T. The challenge of intracellular temperature. Biophys Rev 2020; 12:593-600. [PMID: 32172449 PMCID: PMC7242542 DOI: 10.1007/s12551-020-00683-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023] Open
Abstract
This short review begins with a brief introductory summary of luminescence nanothermometry. Current applications of luminescence nanothermometry are introduced in biological contexts. Then, theoretical bases of the “temperature” that luminescence nanothermometry determines are discussed. This argument is followed by the 105 gap issue between simple calculation and the measurements reported in literatures. The gap issue is challenged by recent literatures reporting single-cell thermometry using non-luminescent probes, as well as a report that determines the thermal conductivity of a single lipid bilayer using luminescence nanothermometry. In the end, we argue if we can be optimistic about the solution of the 105 gap issue.
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Affiliation(s)
- Madoka Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Taras Plakhotnik
- School of Mathematics and Physics, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
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22
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Nanoscale Quantum Thermal Conductance at Water Interface: Green's Function Approach Based on One-Dimensional Phonon Model. Molecules 2020; 25:molecules25051185. [PMID: 32151110 PMCID: PMC7179406 DOI: 10.3390/molecules25051185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/17/2020] [Accepted: 02/25/2020] [Indexed: 12/27/2022] Open
Abstract
We have derived the fundamental formula of phonon transport in water for the evaluation of quantum thermal conductance by using a one-dimensional phonon model based on the nonequilibrium Green’s function method. In our model, phonons are excited as quantum waves from the left or right reservoir and propagate from left to right of H2O layer or vice versa. We have assumed these reservoirs as being of periodic structures, whereas we can also model the H2O sandwiched between these reservoirs as having aperiodic structures of liquid containing N water molecules. We have extracted the dispersion curves from the experimental absorption spectra of the OH stretching and intermolecular modes of water molecules, and calculated phonon transmission function and quantum thermal conductance. In addition, we have simplified the formulation of the transmission function by employing a case of one water molecule (N=1). From this calculation, we have obtained the characteristic that the transmission probability is almost unity at the frequency bands of acoustic and optical modes, and the transmission probability vanishes by the phonon attenuation reflecting the quantum tunnel effect outside the bands of these two modes. The classical limit of the thermal conductance calculated by our formula agreed with the literature value (order of 10−10 W/K) in high temperature regime (>300 K). The present approach is powerful enough to be applicable to molecular systems containing proteins as well, and to evaluate their thermal conductive characteristics.
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23
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de Miguel R, Rubí JM. Negative Thermophoretic Force in the Strong Coupling Regime. PHYSICAL REVIEW LETTERS 2019; 123:200602. [PMID: 31809117 DOI: 10.1103/physrevlett.123.200602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Negative thermophoresis (a particle moving up the temperature gradient) is a somewhat counterintuitive phenomenon which has thus far eluded a simple thermostatistical description. The purpose of this Letter is to show that a thermodynamic framework based on the formulation of a Hamiltonian of mean force has the descriptive ability to capture this interesting and elusive phenomenon in an unusually elegant and straightforward fashion. We propose a mechanism that describes the advent of a thermophoretic force acting from cold to hot on systems that are strongly coupled to a nonisothermal heat bath. When a system is strongly coupled to the heat bath, the system's eigenenergies E_{j} become effectively temperature dependent. This adjustment of the energy levels allows the system to take heat from the environment, +d⟨E_{j}⟩, and return it as work, -d⟨TdE_{j}/dT⟩. This effect can make the temperature dependence of the effective energy profile nonmonotonic. As a result, particles may experience a force in either direction depending on the temperature.
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Affiliation(s)
- Rodrigo de Miguel
- Department of Teacher Education, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - J Miguel Rubí
- Department of Condensed Matter Physics, University of Barcelona, E-08028 Barcelona, Spain
- PoreLab-Center of Excellence, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
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24
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Leitner DM, Pandey HD, Reid KM. Energy Transport across Interfaces in Biomolecular Systems. J Phys Chem B 2019; 123:9507-9524. [DOI: 10.1021/acs.jpcb.9b07086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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25
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Zavyalova E, Kopylov A. Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions. Molecules 2019; 24:molecules24071443. [PMID: 30979095 PMCID: PMC6480146 DOI: 10.3390/molecules24071443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Many nucleic acid–protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer–protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid–protein structures discriminated peculiarities of high-affinity nucleic acid–protein complexes. The size of the amino acid sidechain in the interface was demonstrated to be the most significant parameter that correlates with affinity of aptamers. This observation could be explained in terms of need of efficient energy transfer from interacting residues. Application of energy dissipation theory provided an illustrative tool for estimation of efficiency of aptamer–protein complexes. These results are of great importance for a design of efficient aptamers.
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Affiliation(s)
| | - Alexey Kopylov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.
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26
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Rajabpour A, Seif R, Arabha S, Heyhat MM, Merabia S, Hassanali A. Thermal transport at a nanoparticle-water interface: A molecular dynamics and continuum modeling study. J Chem Phys 2019; 150:114701. [DOI: 10.1063/1.5084234] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ali Rajabpour
- Advanced Simulation and Computing Laboratory, Imam Khomeini International University, Qazvin, Iran
| | - Roham Seif
- Advanced Simulation and Computing Laboratory, Imam Khomeini International University, Qazvin, Iran
- Dipartimento di Energia, Politecnico di Milano, Via Lambruschini 4, 20156 Milano, Italy
| | - Saeed Arabha
- Advanced Simulation and Computing Laboratory, Imam Khomeini International University, Qazvin, Iran
| | - Mohammad Mahdi Heyhat
- Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Samy Merabia
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Ali Hassanali
- International Centre for Theoretical Physics (ICTP), Trieste, Italy
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27
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Duret G, Polali S, Anderson ED, Bell AM, Tzouanas CN, Avants BW, Robinson JT. Magnetic Entropy as a Proposed Gating Mechanism for Magnetogenetic Ion Channels. Biophys J 2019; 116:454-468. [PMID: 30665695 PMCID: PMC6369444 DOI: 10.1016/j.bpj.2019.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/22/2018] [Accepted: 01/02/2019] [Indexed: 12/25/2022] Open
Abstract
Magnetically sensitive ion channels would allow researchers to better study how specific brain cells affect behavior in freely moving animals; however, recent reports of "magnetogenetic" ion channels based on biogenic ferritin nanoparticles have been questioned because known biophysical mechanisms cannot explain experimental observations. Here, we reproduce a weak magnetically mediated calcium response in HEK cells expressing a previously published TRPV4-ferritin fusion protein. We find that this magnetic sensitivity is attenuated when we reduce the temperature sensitivity of the channel but not when we reduce the mechanical sensitivity of the channel, suggesting that the magnetic sensitivity of this channel is thermally mediated. As a potential mechanism for this thermally mediated magnetic response, we propose that changes in the magnetic entropy of the ferritin particle can generate heat via the magnetocaloric effect and consequently gate the associated temperature-sensitive ion channel. Unlike other forms of magnetic heating, the magnetocaloric mechanism can cool magnetic particles during demagnetization. To test this prediction, we constructed a magnetogenetic channel based on the cold-sensitive TRPM8 channel. Our observation of a magnetic response in cold-gated channels is consistent with the magnetocaloric hypothesis. Together, these new data and our proposed mechanism of action provide additional resources for understanding how ion channels could be activated by low-frequency magnetic fields.
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Affiliation(s)
- Guillaume Duret
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas
| | - Sruthi Polali
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas; Applied Physics Program, Rice University, Houston, Texas
| | - Erin D Anderson
- Department of Bioengineering, Rice University, Houston, Texas
| | - A Martin Bell
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas; Applied Physics Program, Rice University, Houston, Texas
| | | | - Benjamin W Avants
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas
| | - Jacob T Robinson
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Applied Physics Program, Rice University, Houston, Texas; Department of Neuroscience, Baylor College of Medicine, Houston, Texas.
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28
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Pandey HD, Leitner DM. Small Saccharides as a Blanket around Proteins: A Computational Study. J Phys Chem B 2018; 122:7277-7285. [DOI: 10.1021/acs.jpcb.8b04632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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29
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Okabe K, Sakaguchi R, Shi B, Kiyonaka S. Intracellular thermometry with fluorescent sensors for thermal biology. Pflugers Arch 2018; 470:717-731. [PMID: 29397424 PMCID: PMC5942359 DOI: 10.1007/s00424-018-2113-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/27/2022]
Abstract
Temperature influences the activities of living organisms at various levels. Cells not only detect environmental temperature changes through their unique temperature-sensitive molecular machineries but also muster an appropriate response to the temperature change to maintain their inherent functions. Despite the fundamental involvement of temperature in physiological phenomena, the mechanism by which cells produce and use heat is largely unknown. Recently, fluorescent thermosensors that function as thermometers in live cells have attracted much attention in biology. These new tools, made of various temperature-sensitive molecules, have allowed for intracellular thermometry at the single-cell level. Intriguing spatiotemporal temperature variations, including organelle-specific thermogenesis, have been revealed with these fluorescent thermosensors, which suggest an intrinsic connection between temperature and cell functions. Moreover, fluorescent thermosensors have shown that intracellular temperature changes at the microscopic level are largely different from those assumed for a water environment at the macroscopic level. Thus, the employment of fluorescent thermosensors will uncover novel mechanisms of intracellular temperature-assisted physiological functions.
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Affiliation(s)
- Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- JST, PRESTO, 4-8-1 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Reiko Sakaguchi
- World Premier International Research Initiative-Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Beini Shi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
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30
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Youssefian S, Rahbar N, Lambert CR, Van Dessel S. Variation of thermal conductivity of DPPC lipid bilayer membranes around the phase transition temperature. J R Soc Interface 2018; 14:rsif.2017.0127. [PMID: 28539484 PMCID: PMC5454301 DOI: 10.1098/rsif.2017.0127] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/26/2017] [Indexed: 01/28/2023] Open
Abstract
Given their amphiphilic nature and chemical structure, phospholipids exhibit a strong thermotropic and lyotropic phase behaviour in an aqueous environment. Around the phase transition temperature, phospholipids transform from a gel-like state to a fluid crystalline structure. In this transition, many key characteristics of the lipid bilayers such as structure and thermal properties alter. In this study, we employed atomistic simulation techniques to study the structure and underlying mechanisms of heat transfer in dipalmitoylphosphatidylcholine (DPPC) lipid bilayers around the fluid–gel phase transformation. To investigate this phenomenon, we performed non-equilibrium molecular dynamics simulations for a range of different temperature gradients. The results show that the thermal properties of the DPPC bilayer are highly dependent on the temperature gradient. Higher temperature gradients cause an increase in the thermal conductivity of the DPPC lipid bilayer. We also found that the thermal conductivity of DPPC is lowest at the transition temperature whereby one lipid leaflet is in the gel phase and the other is in the liquid crystalline phase. This is essentially related to a growth in thermal resistance between the two leaflets of lipid at the transition temperature. These results provide significant new insights into developing new thermal insulation for engineering applications.
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Affiliation(s)
- Sina Youssefian
- Civil and Environmental Engineering Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Nima Rahbar
- Civil and Environmental Engineering Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Christopher R Lambert
- Chemistry and Biochemistry Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Steven Van Dessel
- Civil and Environmental Engineering Department, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
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31
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Ram Lamichhane T, Prasad Lamichhane H. Heat conduction by thyroid hormone receptors. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.4.245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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32
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Abstract
Understanding how small systems exchange energy with a heat bath is important to describe how their unique properties can be affected by the environment. In this contribution, we apply Landsberg's theory of temperature-dependent energy levels to describe the progressive thermalization of small systems as their spectrum is perturbed by a heat bath. We propose a mechanism whereby the small system undergoes a discrete series of excitations and isentropic spectrum adjustments leading to a final state of thermal equilibrium. This produces standard thermodynamic results without invoking system size. The thermal relaxation of a single harmonic oscillator is analyzed as a model example of a system with a quantized spectrum than can be embedded in a thermal environment. A description of how the thermal environment affects the spectrum of a small system can be the first step in using environmental factors, such as temperature, as parameters in the design and operation of nanosystem properties.
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Affiliation(s)
- Rodrigo de Miguel
- Department of Teacher Education, Norwegian University of Science and Technology , 7491 Trondheim, Norway
| | - J Miguel Rubí
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona , 08029 Barcelona, Spain
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33
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Levenberg A, Shafiei G, Lujan MA, Giannacopoulos S, Picorel R, Zazubovich V. Probing Energy Landscapes of Cytochrome b 6f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent. J Phys Chem B 2017; 121:9848-9858. [PMID: 28956922 DOI: 10.1021/acs.jpcb.7b07686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In non-photochemical spectral hole burning (NPHB) and spectral hole recovery experiments, cytochrome b6f protein exhibits behavior that is almost independent of the deuteration of the buffer/glycerol glassy matrix containing the protein, apart from some differences in heat dissipation. On the other hand, strong dependence of the hole burning properties on sample preparation procedures was observed and attributed to a large increase of the electron-phonon coupling and shortening of the excited-state lifetime occurring when n-dodecyl β-d-maltoside (DM) is used as a detergent instead of n-octyl β-d-glucopyranoside (OGP). The data was analyzed assuming that the tunneling parameter distribution or barrier distribution probed by NPHB and encoded into the spectral holes contains contributions from two nonidentical components with accidentally degenerate excited state λ-distributions. Both components likely reflect protein dynamics, although with some small probability one of them (with larger md2) may still represent the dynamics involving specifically the -OH groups of the water/glycerol solvent. Single proton tunneling in the water/glycerol solvent environment or in the protein can be safely excluded as the origin of observed NPHB and hole recovery dynamics. The intensity dependence of the hole growth kinetics in deuterated samples likely reflects differences in heat dissipation between protonated and deuterated samples. These differences are most probably due to the higher interface thermal resistivity between (still protonated) protein and deuterated water/glycerol outside environment.
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Affiliation(s)
- Alexander Levenberg
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Golia Shafiei
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Maria A Lujan
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005, 50059 Zaragoza, Spain
| | - Steven Giannacopoulos
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005, 50059 Zaragoza, Spain
| | - Valter Zazubovich
- Department of Physics, Concordia University , 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
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34
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Muscatello J, Chacón E, Tarazona P, Bresme F. Deconstructing Temperature Gradients across Fluid Interfaces: The Structural Origin of the Thermal Resistance of Liquid-Vapor Interfaces. PHYSICAL REVIEW LETTERS 2017; 119:045901. [PMID: 29341757 DOI: 10.1103/physrevlett.119.045901] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 06/07/2023]
Abstract
The interfacial thermal resistance determines condensation-evaporation processes and thermal transport across material-fluid interfaces. Despite its importance in transport processes, the interfacial structure responsible for the thermal resistance is still unknown. By combining nonequilibrium molecular dynamics simulations and interfacial analyses that remove the interfacial thermal fluctuations we show that the thermal resistance of liquid-vapor interfaces is connected to a low density fluid layer that is adsorbed at the liquid surface. This thermal resistance layer (TRL) defines the boundary where the thermal transport mechanism changes from that of gases (ballistic) to that characteristic of dense liquids, dominated by frequent particle collisions involving very short mean free paths. We show that the thermal conductance is proportional to the number of atoms adsorbed in the TRL, and hence we explain the structural origin of the thermal resistance in liquid-vapor interfaces.
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Affiliation(s)
- Jordan Muscatello
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Enrique Chacón
- Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Inés de la Cruz 3, E-28049 Madrid, Spain
| | - Pedro Tarazona
- Departamento de Física Teórica de la Materia Condensada, IFIMAC Condensed Matter Physics Center, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Fernando Bresme
- Department of Chemistry, Imperial College London, SW7 2AZ London, United Kingdom
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35
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Zhang T, Gans-Forrest AR, Lee E, Zhang X, Qu C, Pang Y, Sun F, Luo T. Role of Hydrogen Bonds in Thermal Transport across Hard/Soft Material Interfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:33326-33334. [PMID: 27934170 DOI: 10.1021/acsami.6b12073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The nature of the bond is a dominant factor in determining the thermal transport across interfaces. In this paper, we study the role of the hydrogen bond in thermal transport across interfaces between hard and soft materials with different surface functionalizations around room temperature using molecular dynamics simulations. Gold (Au) is studied as the hard material, and four different types of organic liquids with different polarizations, including hexane (C5H11CH3), hexanamine (C6H13NH2), hexanol (C6H13OH), and hexanoic acid (C5H11COOH), are used to represent the soft materials. To study the hydrogen bonds at the Au/organic liquid interface, three types of thiol-terminated self-assembled monolayer (SAM) molecules, including 1-hexanethiol [HS(CH2)5CH3], 6-mercapto-1-hexanol [HS(CH2)6OH], and 6-mercaptohexanoic acid [HS(CH2)5COOH], are used to functionalize the Au surface. These SAM molecules form hydrogen bonds with the studied organic liquids with varying strengths, which are found to significantly improve efficient interfacial thermal transport. Detailed analyses on the molecular-level details reveal that such efficient thermal transport originates from the collaborative effects of the electrostatic and van der Waals portions in the hydrogen bonds. It is found that stronger hydrogen bonds will pull the organic molecules closer to the interface. This shorter intermolecular distance leads to increased interatomic forces across the interfaces, which result in larger interfacial heat flux and thus higher thermal conductance. These results can provide important insight into the design of hard/soft materials or structures for a wide range of applications.
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Affiliation(s)
| | | | | | | | | | | | - Fangyuan Sun
- Institute of Engineering Thermophysics, Chinese Academy of Sciences , Beijing 100190, China
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36
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Intercalated water layers promote thermal dissipation at bio-nano interfaces. Nat Commun 2016; 7:12854. [PMID: 27659484 PMCID: PMC5036148 DOI: 10.1038/ncomms12854] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/09/2016] [Indexed: 01/18/2023] Open
Abstract
The increasing interest in developing nanodevices for biophysical and biomedical applications results in concerns about thermal management at interfaces between tissues and electronic devices. However, there is neither sufficient knowledge nor suitable tools for the characterization of thermal properties at interfaces between materials of contrasting mechanics, which are essential for design with reliability. Here we use computational simulations to quantify thermal transfer across the cell membrane–graphene interface. We find that the intercalated water displays a layered order below a critical value of ∼1 nm nanoconfinement, mediating the interfacial thermal coupling, and efficiently enhancing the thermal dissipation. We thereafter develop an analytical model to evaluate the critical value for power generation in graphene before significant heat is accumulated to disturb living tissues. These findings may provide a basis for the rational design of wearable and implantable nanodevices in biosensing and thermotherapic treatments where thermal dissipation and transport processes are crucial. Thermal management is important for designing bio-nano interfaces for biosensing and thermotherapic applications. Here the authors perform simulations showing that nm-thick water layers between graphene and cell membranes display layered ordering, promoting interfacial thermal coupling and thermal dissipation.
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37
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Jackson N, Rubi JM, Bresme F. Non-equilibrium molecular dynamics simulations of the thermal transport properties of Lennard-Jones fluids using configurational temperatures. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1168926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Niall Jackson
- Department of Chemistry, Imperial College London, London, UK
- Thomas Young Centre for Theory and Simulation of Materials, Imperial College, London, UK
| | - J. Miguel Rubi
- Departmento de Fisica, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Fernando Bresme
- Department of Chemistry, Imperial College London, London, UK
- Thomas Young Centre for Theory and Simulation of Materials, Imperial College, London, UK
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
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38
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Nishimura T, Mori F, Hanida S, Kumahata K, Ishikawa S, Samarat K, Miyabe-Nishiwaki T, Hayashi M, Tomonaga M, Suzuki J, Matsuzawa T, Matsuzawa T. Impaired Air Conditioning within the Nasal Cavity in Flat-Faced Homo. PLoS Comput Biol 2016; 12:e1004807. [PMID: 27010321 PMCID: PMC4807068 DOI: 10.1371/journal.pcbi.1004807] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 02/11/2016] [Indexed: 11/18/2022] Open
Abstract
We are flat-faced hominins with an external nose that protrudes from the face. This feature was derived in the genus Homo, along with facial flattening and reorientation to form a high nasal cavity. The nasal passage conditions the inhaled air in terms of temperature and humidity to match the conditions required in the lung, and its anatomical variation is believed to be evolutionarily sensitive to the ambient atmospheric conditions of a given habitat. In this study, we used computational fluid dynamics (CFD) with three-dimensional topology models of the nasal passage under the same simulation conditions, to investigate air-conditioning performance in humans, chimpanzees, and macaques. The CFD simulation showed a horizontal straight flow of inhaled air in chimpanzees and macaques, contrasting with the upward and curved flow in humans. The inhaled air is conditioned poorly in humans compared with nonhuman primates. Virtual modifications to the human external nose topology, in which the nasal vestibule and valve are modified to resemble those of chimpanzees, change the airflow to be horizontal, but have little influence on the air-conditioning performance in humans. These findings suggest that morphological variation of the nasal passage topology was only weakly sensitive to the ambient atmosphere conditions; rather, the high nasal cavity in humans was formed simply by evolutionary facial reorganization in the divergence of Homo from the other hominin lineages, impairing the air-conditioning performance. Even though the inhaled air is not adjusted well within the nasal cavity in humans, it can be fully conditioned subsequently in the pharyngeal cavity, which is lengthened in the flat-faced Homo. Thus, the air-conditioning faculty in the nasal passages was probably impaired in early Homo members, although they have survived successfully under the fluctuating climate of the Plio-Pleistocene, and then they moved “Out of Africa” to explore the more severe climates of Eurasia. This is the first investigation of nasal air conditioning in nonhuman hominoids based on computational fluid dynamics with digital topological models of the nasal passage made using medical imaging. Our comparative results of humans, chimpanzees, and macaques show that the inhaled air is conditioned poorly in humans compared with nonhuman primates. We also show that our protruding external nose has little effect on improving air conditioning. The nasal anatomy in Homo was weakly sensitive to the ambient atmosphere conditions in evolution, but was formed passively by facial reorganization in this genus. Even though the inhaled air is not adjusted well within the nasal cavity in humans, it can be fully conditioned subsequently in the pharyngeal cavity, which is lengthened in flat-faced Homo. Thus, despite an impaired air-conditioning conformation in the nasal passages, Homo members must have survived successfully under the fluctuating climate of the Plio-Pleistocene, and then they moved “Out of Africa” in the Early Pleistocene to explore the more severe climates and ecological environments of Eurasia.
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Affiliation(s)
- Takeshi Nishimura
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
- * E-mail:
| | - Futoshi Mori
- Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Iwate, Japan
| | - Sho Hanida
- Kanazawa Institute of Technology, Nonoichi, Ishikawa, Japan
| | - Kiyoshi Kumahata
- RIKEN Advanced Institute for Computational Science, Kobe, Hyogo, Japan
| | | | - Kaouthar Samarat
- Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
| | | | - Misato Hayashi
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Masaki Tomonaga
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Juri Suzuki
- Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | | | - Teruo Matsuzawa
- Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
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39
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Inoue Y, Ishijima A. Local heating of molecular motors using single carbon nanotubes. Biophys Rev 2016; 8:25-32. [PMID: 28510142 DOI: 10.1007/s12551-015-0185-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/26/2015] [Indexed: 12/11/2022] Open
Abstract
Temperature globally affects all chemical processes and biomolecules in living cells. Elevating the temperature of an entire cell accelerates so many biomolecular reactions simultaneously that it is difficult to distinguish the various mechanisms involved. The ability to localize temperature changes to the nanometer range within a cell could provide a powerful new tool for regulating biomolecular activity at the level of individual molecules. The search for a nanoheater for biological research has prompted experiments with carbon nanotubes (CNTs), which have the highest conductivity of any known material. The adsorption of skeletal muscle myosin molecules along the length of single multi-walled CNTs (~10 μm) has allowed researchers to observe the ATP-driven sliding of fluorescently labeled actin filaments. In one study, red-laser irradiation focused on one end of a myosin-coated CNT was used to heat myosin motors locally without directly heating the surrounding water; this laser irradiation instantly accelerated the actin-filament sliding speeds from ~6 to ~12 μm/s in a reversible manner, indicating a local, real-time heating of myosin motors by approximately Δ12 K. Calculation of heat transfer using the finite element method, based on the estimated temperature along a single CNT with a diameter of 170 nm, indicated a high thermal conductivity of ~1540 Wm-1K-1 in solution, consistent with values measured in vacuum in earlier studies. Temperature distribution indicated by half-decrease distances was ~3660 nm along the length of the CNT and ~250 nm perpendicular to the length. These results suggest that single-CNT-based heating at the nanometer- or micrometer-range could be used to regulate various biomolecules in many areas of biological, physical, and chemical research.
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Affiliation(s)
- Yuichi Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Akihiko Ishijima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan. .,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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40
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41
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Validating subcellular thermal changes revealed by fluorescent thermosensors. Nat Methods 2015; 12:801-2. [DOI: 10.1038/nmeth.3548] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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42
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Santamaría-Holek I, López-Alamilla NJ, Hidalgo-Soria M, Pérez-Madrid A. Nonlinear irreversible thermodynamics of single-molecule experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:062714. [PMID: 26172743 DOI: 10.1103/physreve.91.062714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Indexed: 06/04/2023]
Abstract
Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the nonlinear case of systems under nonequilibrium external constraints, we are able to calculate the entropy production and the general nonlinear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.
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Affiliation(s)
- I Santamaría-Holek
- UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México
| | - N J López-Alamilla
- UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México
| | - M Hidalgo-Soria
- UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México
| | - A Pérez-Madrid
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Marti i Franques, 08028 Barcelona, Spain
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43
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Mori F, Hanida S, Kumahata K, Miyabe-Nishiwaki T, Suzuki J, Matsuzawa T, Nishimura TD. Minor contributions of the maxillary sinus to the air-conditioning performance in macaque monkeys. ACTA ACUST UNITED AC 2015; 218:2394-401. [PMID: 26034122 DOI: 10.1242/jeb.118059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/18/2015] [Indexed: 11/20/2022]
Abstract
The nasal passages mainly adjust the temperature and humidity of inhaled air to reach the alveolar condition required in the lungs. By contrast to most other non-human primates, macaque monkeys are distributed widely among tropical, temperate and subarctic regions, and thus some species need to condition the inhaled air in cool and dry ambient atmospheric areas. The internal nasal anatomy is believed to have undergone adaptive modifications to improve the air-conditioning performance. Furthermore, the maxillary sinus (MS), an accessory hollow communicating with the nasal cavity, is found in macaques, whereas it is absent in most other extant Old World monkeys, including savanna monkeys. In this study, we used computational fluid dynamics simulations to simulate the airflow and heat and water exchange over the mucosal surface in the nasal passage. Using the topology models of the nasal cavity with and without the MS, we demonstrated that the MS makes little contribution to the airflow pattern and the air-conditioning performance within the nasal cavity in macaques. Instead, the inhaled air is conditioned well in the anterior portion of the nasal cavity before reaching the MS in both macaques and savanna monkeys. These findings suggest that the evolutionary modifications and coetaneous variations in the nasal anatomy are rather independent of transitions and variations in the climate and atmospheric environment found in the habitats of macaques.
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Affiliation(s)
- Futoshi Mori
- Interfaculty Initiative in Information Studies, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan Earthquake Research Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Sho Hanida
- Kanazawa Institute of Technology, Nonoichi, Ishikawa 921-8501, Japan
| | - Kiyoshi Kumahata
- RIKEN Advanced Institute for Computational Science, Kobe, Hyogo 650-0047, Japan
| | | | - Juri Suzuki
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Teruo Matsuzawa
- Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
| | - Takeshi D Nishimura
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
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44
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Leitner DM, Buchenberg S, Brettel P, Stock G. Vibrational energy flow in the villin headpiece subdomain: Master equation simulations. J Chem Phys 2015; 142:075101. [DOI: 10.1063/1.4907881] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Paul Brettel
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Gerhard Stock
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
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45
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Abstract
The relaxation of coherence in vibrational energy transport in molecules is investigated.
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Affiliation(s)
- Zhedong Zhang
- Department of Physics and Astronomy
- SUNY Stony Brook
- Stony Brook
- USA
| | - Jin Wang
- Department of Physics and Astronomy
- SUNY Stony Brook
- Stony Brook
- USA
- Department of Chemistry
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46
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Alicki R, Leitner DM. Size-Dependent Accuracy of Nanoscale Thermometers. J Phys Chem B 2014; 119:9000-5. [DOI: 10.1021/jp508047q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Robert Alicki
- Institute
of Theoretical Physics and Astrophysics, University of Gdansk, Gdansk, Poland
- Freiburg
Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - David M. Leitner
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
- Freiburg
Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
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47
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Nguyen SC, Lomont JP, Caplins BW, Harris CB. Studying the Dynamics of Photochemical Reactions via Ultrafast Time-Resolved Infrared Spectroscopy of the Local Solvent. J Phys Chem Lett 2014; 5:2974-2978. [PMID: 26278245 DOI: 10.1021/jz501400t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Conventional ultrafast spectroscopic studies on the dynamics of chemical reactions in solution directly probe the solute undergoing the reaction. We provide an alternative method for probing reaction dynamics via monitoring of the surrounding solvent. When the reaction exchanges the energy (in form of heat) with the solvent, the absorption cross sections of the solvent's infrared bands are sensitive to the heat transfer, allowing spectral tracking of the reaction dynamics. This spectroscopic technique was demonstrated to be able to distinguish the differing photoisomerization dynamics of the trans and cis isomers of stilbene in acetonitrile solution. We highlight the potential of this spectroscopic approach for studying the dynamics of chemical reactions or other heat transfer processes when probing the solvent is more experimentally feasible than probing the solute directly.
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Affiliation(s)
- Son C Nguyen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Justin P Lomont
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Benjamin W Caplins
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Charles B Harris
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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48
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Miño G, Barriga R, Gutierrez G. Hydrogen Bonds and Heat Diffusion in α-Helices: A Computational Study. J Phys Chem B 2014; 118:10025-34. [DOI: 10.1021/jp503420e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- German Miño
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
- Centro
Interdisciplinario de Neurociencias de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile
- Facultad
de Ciencias Biologicas, Centro de Bioinformatica y Biologia Integrativa, Universidad Andres Bello, Av.Republica 239, Santiago, Chile
| | - Raul Barriga
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Gonzalo Gutierrez
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
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49
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Agbo JK, Xu Y, Zhang P, Straub JE, Leitner DM. Vibrational energy flow across heme–cytochrome c and cytochrome c–water interfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1504-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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50
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Gong F, Hongyan Z, Papavassiliou DV, Bui K, Lim C, Duong HM. Mesoscopic modeling of cancer photothermal therapy using single-walled carbon nanotubes and near infrared radiation: insights through an off-lattice Monte Carlo approach. NANOTECHNOLOGY 2014; 25:205101. [PMID: 24784034 DOI: 10.1088/0957-4484/25/20/205101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Single-walled carbon nanotubes (SWNTs) are promising heating agents in cancer photothermal therapy when under near infrared radiation, yet few efforts have been focused on the quantitative understanding of the photothermal energy conversion in biological systems. In this article, a mesoscopic study that takes into account SWNT morphologies (diameter and aspect ratio) and dispersions (orientation and concentration), as well as thermal boundary resistance, is performed by means of an off-lattice Monte Carlo simulation. Results indicate that SWNTs with orientation perpendicular to the laser, smaller diameter and better dispersion have higher heating efficiency in cancer photothermal therapy. Thermal boundary resistances greatly inhibit thermal energy transfer away from SWNTs, thereby affecting their heating efficiency. Through appropriate interfacial modification around SWNTs, compared to the surrounding healthy tissue, a higher temperature of the cancer cell can be achieved, resulting in more effective cancer photothermal therapy. These findings promise to bridge the gap between macroscopic and microscopic computational studies of cancer photothermal therapy.
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Affiliation(s)
- Feng Gong
- Department of Mechanical Engineering, National University of Singapore, 117576, Singapore
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