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Madrid I, Zheng Z, Gerbelot C, Fujiwara A, Li S, Grall S, Nishiguchi K, Kim SH, Chovin A, Demaille C, Clement N. Ballistic Brownian Motion of Nanoconfined DNA. ACS NANO 2023; 17:17031-17040. [PMID: 37700490 DOI: 10.1021/acsnano.3c04349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Theoretical treatments of polymer dynamics in liquid generally start with the basic assumption that motion at the smallest scale is heavily overdamped; therefore, inertia can be neglected. We report on the Brownian motion of tethered DNA under nanoconfinement, which was analyzed by molecular dynamics simulation and nanoelectrochemistry-based single-electron shuttle experiments. Our results show a transition into the ballistic Brownian motion regime for short DNA in sub-5 nm gaps, with quality coefficients as high as 2 for double-stranded DNA, an effect mainly attributed to a drastic increase in stiffness. The possibility for DNA to enter the underdamped regime could have profound implications on our understanding of the energetics of biomolecular engines such as the replication machinery, which operates in nanocavities that are a few nanometers wide.
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Affiliation(s)
- Ignacio Madrid
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Zhiyong Zheng
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Cedric Gerbelot
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Akira Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Shuo Li
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Simon Grall
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Katsuhiko Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
| | - Soo Hyeon Kim
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
| | - Arnaud Chovin
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Christophe Demaille
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Nicolas Clement
- IIS, LIMMS CNRS-IIS UMI2820, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo 153-8505, Japan
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato-Wakamiya, Atsugi-shi 243-0198, Japan
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2
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Sun Z, Kalhor P, Xu Y, Liu J. Extensive numerical tests of leapfrog integrator in middle thermostat scheme in molecular simulations. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2111242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing 100871, China
| | - Payam Kalhor
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing 100871, China
| | - Yang Xu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing 100871, China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing 100871, China
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3
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Mahalingam V, Harursampath D. Effect of the Base-Pair Sequence on B-DNA Thermal Conductivity. J Phys Chem B 2021; 125:10652-10656. [PMID: 34533965 DOI: 10.1021/acs.jpcb.1c04318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thermal conductivity of double-stranded (ds) B-DNA was systematically investigated using classical molecular dynamics (MD) simulations. The effect of changing the base pair (bp) on the thermal conductivity of dsDNA needed investigation at a molecular level. Hence, four sequences, viz., poly(A), poly(G), poly(CG), and poly(AT), were initially analyzed in this work. First, the length of these sequences was varied from 4 to 40 bp at 300 K, and the respective thermal conductivity (κ) was computed. Second, the temperature-dependent thermal conductivities between 100 and 400 K were obtained in 50 K steps at 28 bp length. The Müller-Plathe reverse nonequilibrium molecular dynamics (RNEMD) was employed to set a thermal gradient and obtain all thermal conductivities in this work. Moreover, mixed sequences using AT and CG sequences, namely, A(CG)nT (n = 3-7), ACGC(AT)mGCGT (m = 0-5), and ACGC(AT)nAGCGT (n = 1-4), were investigated based on the hypothesis that these sequences could be better thermoelectrics. One-dimensional lattices are said to have diverging thermal conductivities at longer lengths, which violate the Fourier law. These follow the power law, where κ ∝ Lβ. At longer lengths, the exponent β needs to satisfy the condition β > 1/3 for divergent thermal conductivity. We find no such significant Fourier law violation through divergence of thermal conductivities at 80 bp lengths or 40 bp lengths. Also, in the case of the second study, the presence of short (m ≤ 2) encapsulated AT sequences within CG sequences shows an increasing trend. These results are important for engineering DNA-based thermal devices.
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Affiliation(s)
- Vignesh Mahalingam
- Department of Aerospace Engineering, Indian Institute of Science, Bengaluru 560012, India
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4
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Elenewski JE, Wójtowicz G, Rams MM, Zwolak M. Performance of reservoir discretizations in quantum transport simulations. J Chem Phys 2021; 155:124117. [PMID: 34598565 DOI: 10.1063/5.0065799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Quantum transport simulations often use explicit, yet finite, electronic reservoirs. These should converge to the correct continuum limit, albeit with a trade-off between discretization and computational cost. Here, we study this interplay for extended reservoir simulations, where relaxation maintains a bias or temperature drop across the system. Our analysis begins in the non-interacting limit, where we parameterize different discretizations to compare them on an even footing. For many-body systems, we develop a method to estimate the relaxation that best approximates the continuum by controlling virtual transitions in Kramers turnover for the current. While some discretizations are more efficient for calculating currents, there is little benefit with regard to the overall state of the system. Any gains become marginal for many-body, tensor network simulations, where the relative performance of discretizations varies when sweeping other numerical controls. These results indicate that typical reservoir discretizations have little impact on numerical costs for certain computational tools. The choice of a relaxation parameter is nonetheless crucial, and the method we develop provides a reliable estimate of the optimal relaxation for finite reservoirs.
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Affiliation(s)
- Justin E Elenewski
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Gabriela Wójtowicz
- Jagiellonian University, Institute of Theoretical Physics, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Marek M Rams
- Jagiellonian University, Institute of Theoretical Physics, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Michael Zwolak
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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5
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Zhang Y, Min C, Dou X, Wang X, Urbach HP, Somekh MG, Yuan X. Plasmonic tweezers: for nanoscale optical trapping and beyond. LIGHT, SCIENCE & APPLICATIONS 2021; 10:59. [PMID: 33731693 PMCID: PMC7969631 DOI: 10.1038/s41377-021-00474-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/24/2020] [Accepted: 01/14/2021] [Indexed: 05/06/2023]
Abstract
Optical tweezers and associated manipulation tools in the far field have had a major impact on scientific and engineering research by offering precise manipulation of small objects. More recently, the possibility of performing manipulation with surface plasmons has opened opportunities not feasible with conventional far-field optical methods. The use of surface plasmon techniques enables excitation of hotspots much smaller than the free-space wavelength; with this confinement, the plasmonic field facilitates trapping of various nanostructures and materials with higher precision. The successful manipulation of small particles has fostered numerous and expanding applications. In this paper, we review the principles of and developments in plasmonic tweezers techniques, including both nanostructure-assisted platforms and structureless systems. Construction methods and evaluation criteria of the techniques are presented, aiming to provide a guide for the design and optimization of the systems. The most common novel applications of plasmonic tweezers, namely, sorting and transport, sensing and imaging, and especially those in a biological context, are critically discussed. Finally, we consider the future of the development and new potential applications of this technique and discuss prospects for its impact on science.
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Affiliation(s)
- Yuquan Zhang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Changjun Min
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.
| | - Xiujie Dou
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
- Optics Research Group, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Xianyou Wang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Hendrik Paul Urbach
- Optics Research Group, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Michael G Somekh
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Xiaocong Yuan
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.
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6
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Abstract
The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical molecular dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D model or a coarse-grained model of DNA to reduce simulation times, full atomistic simulations are employed to understand the thermal conduction in B-DNA. Thermal conductivities at different temperatures from 100 to 400 K are investigated using the Einstein-Green-Kubo equilibrium and Müller-Plathe non-equilibrium formalisms. The thermal conductivity of B-DNA at room temperature is found to be 1.5 W/m·K in equilibrium and 1.225 W/m·K in the non-equilibrium approach. In addition, the denaturation regime of B-DNA is obtained from the variation of thermal conductivity with temperature. It is in agreement with previous studies using the Peyrard-Bishop-Dauxois model at a temperature of around 350 K. The quantum heat capacity (Cvq) has given additional clues regarding the Debye and denaturation temperature of 12-bp B-DNA.
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Affiliation(s)
- Vignesh Mahalingam
- Department of Aerospace Engineering, Indian Institute of Science, Bengaluru 560012, India
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7
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Zwolak M. Analytic expressions for the steady-state current with finite extended reservoirs. J Chem Phys 2020; 153:224107. [PMID: 33317280 PMCID: PMC8356363 DOI: 10.1063/5.0029223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Open-system simulations of quantum transport provide a platform for the study of true steady states, Floquet states, and the role of temperature, time dynamics, and fluctuations, among other physical processes. They are rapidly gaining traction, especially techniques that revolve around "extended reservoirs," a collection of a finite number of degrees of freedom with relaxation that maintains a bias or temperature gradient, and have appeared under various guises (e.g., the extended or mesoscopic reservoir, auxiliary master equation, and driven Liouville-von Neumann approaches). Yet, there are still a number of open questions regarding the behavior and convergence of these techniques. Here, we derive general analytical solutions, and associated asymptotic analyses, for the steady-state current driven by finite reservoirs with proportional coupling to the system/junction. In doing so, we present a simplified and unified derivation of the non-interacting and many-body steady-state currents through arbitrary junctions, including outside of proportional coupling. We conjecture that the analytic solution for proportional coupling is the most general of its form for isomodal relaxation (i.e., relaxing proportional coupling will remove the ability to find compact, general analytical expressions for finite reservoirs). These results should be of broad utility in diagnosing the behavior and implementation of extended reservoir and related approaches, including the convergence to the Landauer limit (for non-interacting systems) and the Meir-Wingreen formula (for many-body systems).
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Affiliation(s)
- Michael Zwolak
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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8
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Jolfaei NA, Jolfaei NA, Hekmatifar M, Piranfar A, Toghraie D, Sabetvand R, Rostami S. Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 185:105169. [PMID: 31715331 DOI: 10.1016/j.cmpb.2019.105169] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Thermal conductivity of Deoxyribonucleic acid molecules is important for nanotechnology applications. Theoretical simulations based on simple models predict thermal conductivity for these molecular structures. METHODS In this work, we calculate the thermal properties of Deoxyribonucleic acid with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches. In these methods, each Deoxyribonucleic acid molecule is represented by C, N, O, and P atoms and implemented dreidng potential to describe their atomic interactions. RESULTS Our calculated rate for thermal conductivity via equilibrium and non-equilibrium molecular dynamics methods is 0.381 W/m K and 0.373 W/m K, respectively. By comparing results from these two methods, it was found that the results from equilibrium and non-equilibrium molecular dynamics methods are identical, approximately. On the other hand, the number of DNA molecules and the equilibrium temperature of the simulated structures were important factors in their thermal conductivity rates, and their thermal conductivity was calculated at 0.323 W/m K-0.381 W/m K intervals for equilibrium and 0.303 W/m K-0.373 W/m K interval for non-equilibrium calculations. CONCLUSIONS These results are in good agreement with thermal conductivity calculation with other research groups.
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Affiliation(s)
| | - Niyusha Adavoodi Jolfaei
- Department of Pharmaceutical Sciences, KLE College of Pharmacy, 2nd block, Rajajinagar, Bengaluru, Karnatka, India
| | - Maboud Hekmatifar
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
| | - Anahita Piranfar
- Biomechanic Department, Biomedical Engineering Faculty, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Davood Toghraie
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
| | - Roozbeh Sabetvand
- Department of Energy Engineering and Physics, Faculty of Condensed Matter Physics, Amirkabir University of Technology, Tehran, Iran
| | - Sara Rostami
- Laboratory of Magnetism and Magnetic Materials, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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9
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Wójtowicz G, Elenewski JE, Rams MM, Zwolak M. Open System Tensor Networks and Kramers' Crossover for Quantum Transport. PHYSICAL REVIEW. A 2020; 101:10.1103/PhysRevA.101.050301. [PMID: 33367191 PMCID: PMC7754794 DOI: 10.1103/physreva.101.050301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tensor networks are a powerful tool for many-body ground states with limited entanglement. These methods can nonetheless fail for certain time-dependent processes-such as quantum transport or quenches-where entanglement growth is linear in time. Matrix-product-state decompositions of the resulting out-of-equilibrium states require a bond dimension that grows exponentially, imposing a hard limit on simulation timescales. However, in the case of transport, if the reservoir modes of a closed system are arranged according to their scattering structure, the entanglement growth can be made logarithmic. Here, we apply this ansatz to open systems via extended reservoirs that have explicit relaxation. This enables transport calculations that can access steady states, time dynamics and noise, and periodic driving (e.g., Floquet states). We demonstrate the approach by calculating the transport characteristics of an open, interacting system. These results open a path to scalable and numerically systematic many-body transport calculations with tensor networks.
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Affiliation(s)
- Gabriela Wójtowicz
- Jagiellonian University, Institute of Theoretical Physics, Lojasiewicza 11, 30-348 Kraków, Poland
| | - Justin E. Elenewski
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
- Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD, USA
| | - Marek M. Rams
- Jagiellonian University, Institute of Theoretical Physics, Lojasiewicza 11, 30-348 Kraków, Poland
| | - Michael Zwolak
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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10
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Topology, landscapes, and biomolecular energy transport. Nat Commun 2019; 10:4662. [PMID: 31604949 PMCID: PMC6789131 DOI: 10.1038/s41467-019-12700-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/12/2019] [Indexed: 12/20/2022] Open
Abstract
While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior that diverges from the macroscale. Here, we show that transient thermal transport reflects macromolecular energy landscape architecture through the topological characteristics of molecular contacts and the nonlinear processes that mediate dynamics. While the former determines transport pathways via pairwise interactions, the latter reflects frustration within the landscape for local conformational rearrangements. Unlike transport through small-molecule systems, such as alkanes, nonlinearity dominates over coherent processes at even quite short time- and length-scales. Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules. The approach demonstrates that vibrational energy transport can probe otherwise inaccessible aspects of macromolecular dynamics and interactions that underly biological function. Understanding vibrational energy transfer in macromolecules has been challenging to both theory and experiment. Here the authors use non-equilibrium molecular dynamics to reveal the relationship between heat transport in a model peptide, emergent nonlinearity, and the underlying free energy landscape.
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11
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Sun Z, Wang X, Zhang JZH, He Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys Chem Chem Phys 2019; 21:14923-14940. [PMID: 31233058 DOI: 10.1039/c9cp01989h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Base flipping is widely observed in a number of important biological processes. The genetic codes deposited inside the DNA duplex become accessible to external agents upon base flipping. The sulfur substitution of guanine leads to thioguanine, which alters the thermodynamic stability of the GC base pairs and the GT mismatches. Experimental studies conclude that the sulfur substitution decreases the lifetime of the GC base pair. In this work, under three AMBER force fields for nucleotide systems, we firstly performed equilibrium and nonequilibrium free energy simulations to investigate the variation of the thermodynamic profiles in base flipping upon sulfur substitution. It is found that the bsc0 modification, the bsc1 modification and the OL15 modification of AMBER force fields are able to qualitatively describe the sulfur-substitution dependent behavior of the thermodynamics. However, only the two last-generation AMBER force fields are able to provide quantitatively correct predictions. The second computational study on the sulfur substitutions focused on the relative stability of the S6G-C base pair and the S6G-T mismatch. Two conflicting experimental observations were reported by the same authors. One suggested that the S6G-C base pair was more stable, while the other concludes that the S6G-T mismatch was more stable. We answered this question by constructing the free energy profiles along the base flipping pathway computationally.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich 52425, Germany.
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Institute of Computational Science, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China and Department of Chemistry, New York University, NY, NY 10003, USA
| | - Qiaole He
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Wilhelm-Johnen-Str. 1, 52425 Jülich, Germany. and State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
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12
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Wang X, Sun Z. Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification. J Chem Inf Model 2019; 59:2980-2994. [PMID: 31124677 DOI: 10.1021/acs.jcim.9b00263] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free-energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free-energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for the efficient calculation of the free-energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free-energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of the equilibrium umbrella sampling and the nonequilibrium stratification is given. The results show that nonequilibrium free-energy simulation achieves similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,Institute of Computational Science , Università della Svizzera Italiana (USI) , Via Giuseppe Buffi 13 , CH-6900 , Lugano , Ticino , Switzerland
| | - Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.,Computational Biomedicine (IAS-5/INM-9) , Forschungszentrum Jülich , Jülich 52425 , Germany
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13
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14
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Chien CC, Velizhanin KA, Dubi Y, Ilic BR, Zwolak M. Topological quantization of energy transport in micro- and nano-mechanical lattices. PHYSICAL REVIEW. B 2018; 97:10.1103/PhysRevB.97.125425. [PMID: 30997441 PMCID: PMC6463522 DOI: 10.1103/physrevb.97.125425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Topological effects typically discussed in the context of quantum physics are emerging as one of the central paradigms of physics. Here, we demonstrate the role of topology in energy transport through dimerized micro- and nano-mechanical lattices in the classical regime, i.e., essentially "masses and springs". We show that the thermal conductance factorizes into topological and nontopological components. The former takes on three discrete values and arises due to the appearance of edge modes that prevent good contact between the heat reservoirs and the bulk, giving a length-independent reduction of the conductance. In essence, energy input at the boundary mostly stays there, an effect robust against disorder and nonlinearity. These results bridge two seemingly disconnected disciplines of physics, namely topology and thermal transport, and suggest ways to engineer thermal contacts, opening a direction to explore the ramifications of topological properties on nanoscale technology.
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Affiliation(s)
- Chih-Chun Chien
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | | | - Yonatan Dubi
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - B. Robert Ilic
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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15
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Chien CC, Kouachi S, Velizhanin KA, Dubi Y, Zwolak M. Thermal transport in dimerized harmonic lattices: Exact solution, crossover behavior, and extended reservoirs. Phys Rev E 2017; 95:012137. [PMID: 28208409 PMCID: PMC5473347 DOI: 10.1103/physreve.95.012137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 11/07/2022]
Abstract
We present a method for calculating analytically the thermal conductance of a classical harmonic lattice with both alternating masses and nearest-neighbor couplings when placed between individual Langevin reservoirs at different temperatures. The method utilizes recent advances in analytic diagonalization techniques for certain classes of tridiagonal matrices. It recovers the results from a previous method that was applicable for alternating on-site parameters only, and extends the applicability to realistic systems in which masses and couplings alternate simultaneously. With this analytic result in hand, we show that the thermal conductance is highly sensitive to the modulation of the couplings. This is due to the existence of topologically induced edge modes at the lattice-reservoir interface and is also a reflection of the symmetries of the lattice. We make a connection to a recent work that demonstrates thermal transport is analogous to chemical reaction rates in solution given by Kramers' theory [Velizhanin et al., Sci. Rep. 5, 17506 (2015)]2045-232210.1038/srep17506. In particular, we show that the turnover behavior in the presence of edge modes prevents calculations based on single-site reservoirs from coming close to the natural-or intrinsic-conductance of the lattice. Obtaining the correct value of the intrinsic conductance through simulation of even a small lattice where ballistic effects are important requires quite large extended reservoir regions. Our results thus offer a route for both the design and proper simulation of thermal conductance of nanoscale devices.
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Affiliation(s)
- Chih-Chun Chien
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Said Kouachi
- Department of Mathematics, Qassim University, Al-Gassim, Buraydah 51452, Saudi Arabia
| | - Kirill A Velizhanin
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Yonatan Dubi
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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Velizhanin KA, Sahu S, Chien CC, Dubi Y, Zwolak M. Crossover behavior of the thermal conductance and Kramers' transition rate theory. Sci Rep 2015; 5:17506. [PMID: 26634333 PMCID: PMC4669443 DOI: 10.1038/srep17506] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/23/2015] [Indexed: 11/26/2022] Open
Abstract
Kramers' theory frames chemical reaction rates in solution as reactants overcoming a barrier in the presence of friction and noise. For weak coupling to the solution, the reaction rate is limited by the rate at which the solution can restore equilibrium after a subset of reactants have surmounted the barrier to become products. For strong coupling, there are always sufficiently energetic reactants. However, the solution returns many of the intermediate states back to the reactants before the product fully forms. Here, we demonstrate that the thermal conductance displays an analogous physical response to the friction and noise that drive the heat current through a material or structure. A crossover behavior emerges where the thermal reservoirs dominate the conductance at the extremes and only in the intermediate region are the intrinsic properties of the lattice manifest. Not only does this shed new light on Kramers' classic turnover problem, this result is significant for the design of devices for thermal management and other applications, as well as the proper simulation of transport at the nanoscale.
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Affiliation(s)
| | - Subin Sahu
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Maryland Nanocenter, University of Maryland, Collage Park, MD 20742, USA
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA
| | - Chih-Chun Chien
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Yonatan Dubi
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA
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Peeters M, van Grinsven B, Cleij TJ, Jiménez-Monroy KL, Cornelis P, Pérez-Ruiz E, Wackers G, Thoelen R, De Ceuninck W, Lammertyn J, Wagner P. Label-free Protein Detection Based on the Heat-Transfer Method--A Case Study with the Peanut Allergen Ara h 1 and Aptamer-Based Synthetic Receptors. ACS APPLIED MATERIALS & INTERFACES 2015; 7:10316-10323. [PMID: 25916249 DOI: 10.1021/acsami.5b00994] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aptamers are an emerging class of molecules that, because of the development of the systematic evolution of ligands by exponential enrichment (SELEX) process, can recognize virtually every target ranging from ions, to proteins, and even whole cells. Although there are many techniques capable of detecting template molecules with aptamer-based systems with high specificity and selectivity, they lack the possibility of integrating them into a compact and portable biosensor setup. Therefore, we will present the heat-transfer method (HTM) as an interesting alternative because this offers detection in a fast and low-cost manner and has the possibility of performing experiments with a fully integrated device. This concept has been demonstrated for a variety of applications including DNA mutation analysis and screening of cancer cells. To the best our knowledge, this is the first report on HTM-based detection of proteins, in this case specifically with aptamer-type receptors. For proof-of-principle purposes, measurements will be performed with the peanut allergen Ara h 1 and results indicate detection limits in the lower nanomolar regime in buffer liquid. As a first proof-of-application, spiked Ara h 1 solutions will be studied in a food matrix of dissolved peanut butter. Reference experiments with the quartz-crystal microbalance will allow for an estimate of the areal density of aptamer molecules on the sensor-chip surface.
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Affiliation(s)
- Marloes Peeters
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ‡School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Bart van Grinsven
- §Maastricht Science Programme, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Thomas J Cleij
- §Maastricht Science Programme, Maastricht University, 6200 MD Maastricht, The Netherlands
| | | | - Peter Cornelis
- ∥Department of Physics and Astronomy, Soft-Matter and Biophysics Section, Catholic University Leuven, Celestijnenlaan 200 D, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- #BIOSYST-MeBioS, KU Leuven-University of Leuven, Willem de Crooylan 42, 3000 Leuven, Belgium
| | - Gideon Wackers
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ∥Department of Physics and Astronomy, Soft-Matter and Biophysics Section, Catholic University Leuven, Celestijnenlaan 200 D, 3001 Leuven, Belgium
| | - Ronald Thoelen
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ⊥Division IMOMEC, IMEC v.z.w. , Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Ward De Ceuninck
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ⊥Division IMOMEC, IMEC v.z.w. , Wetenschapspark 1, 3590 Diepenbeek, Belgium
| | - Jeroen Lammertyn
- #BIOSYST-MeBioS, KU Leuven-University of Leuven, Willem de Crooylan 42, 3000 Leuven, Belgium
| | - Patrick Wagner
- †Institute for Materials Research, Hasselt University, Wetenschapspark 1, 3590 Diepenbeek, Belgium
- ∥Department of Physics and Astronomy, Soft-Matter and Biophysics Section, Catholic University Leuven, Celestijnenlaan 200 D, 3001 Leuven, Belgium
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Fluctuations in the DNA double helix: A critical review. Phys Life Rev 2014; 11:153-70. [PMID: 24560595 DOI: 10.1016/j.plrev.2014.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/27/2013] [Accepted: 12/30/2013] [Indexed: 12/22/2022]
Abstract
A critical overview of the extensive literature on fluctuations in the DNA double helix is presented. Both theory and experiment are comprehensively reviewed and analyzed. Fluctuations, which open up the DNA double helix making bases accessible for hydrogen exchange and chemical modification, are the main focus of the review. Theoretical descriptions of the DNA fluctuations are discussed with special emphasis on most popular among them: the nonlinear-dynamic Peyrard-Bishop-Dauxois (PBD) model and the empirical two-state (or helix-coil) model. The experimental data on the issue are comprehensibly overviewed in the historical retrospective with main emphasis on the hydrogen exchange data and formaldehyde kinetics. The theoretical descriptions are critically evaluated from the viewpoint of their applicability to describe DNA in water environment and from the viewpoint of agreement of their predictions with the reliable experimental data. The presented analysis makes it possible to conclude that, while the two-state model is most adequate from theoretical viewpoint and its predictions, based on an empirical parametrization, agree with experimental data very well, the PBD model is inapplicable to DNA in water from theoretical viewpoint on one hand and it makes predictions totally incompatible with reliable experimental data on the other. In particular, it is argued that any oscillation movements of nucleotides, assumed by the PBD model, are severely damped in water, that no "bubbles", which the PBD model predicts, exist in reality in linear DNA well below the melting range and the lifetime of an open state in DNA is actually 5 orders of magnitude longer than the value predicted by the PBD model.
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Chien CC, Velizhanin KA, Dubi Y, Zwolak M. Tunable thermal switching via DNA-based nano-devices. NANOTECHNOLOGY 2013; 24:095704. [PMID: 23396127 DOI: 10.1088/0957-4484/24/9/095704] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
DNA has a well-defined structural transition--the denaturation of its double-stranded form into two single strands--that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA denaturation, one can engineer DNA 'heattronic' devices that have a rapidly increasing thermal conductance over a narrow temperature range across the denaturation transition (∼350 K). The origin of this rapid increase of conductance, or 'switching', is the softening of the lattice and suppression of nonlinear effects as the temperature crosses the transition temperature and DNA denatures. Most importantly, we demonstrate that DNA nano-junctions have a broad range of thermal tunability by varying the sequence and length, and exploiting the underlying nonlinear behavior. We discuss the role of disorder in the base sequence, as well as the relation to genomic DNA. These results set the basis for developing thermal devices out of materials with nonlinear structural dynamics, as well as understanding the underlying mechanisms of DNA denaturation.
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Affiliation(s)
- Chih-Chun Chien
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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22
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van Grinsven B, Vanden Bon N, Strauven H, Grieten L, Murib M, Monroy KLJ, Janssens SD, Haenen K, Schöning MJ, Vermeeren V, Ameloot M, Michiels L, Thoelen R, De Ceuninck W, Wagner P. Heat-transfer resistance at solid-liquid interfaces: a tool for the detection of single-nucleotide polymorphisms in DNA. ACS NANO 2012; 6:2712-21. [PMID: 22356595 DOI: 10.1021/nn300147e] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA.
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Affiliation(s)
- Bart van Grinsven
- Institute for Materials Research IMO, IMOMEC, Hasselt University, Wetenschapspark 1, B-3590 Diepenbeek, Belgium.
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