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Slongo F, Hauke P, Faccioli P, Micheletti C. Quantum-inspired encoding enhances stochastic sampling of soft matter systems. SCIENCE ADVANCES 2023; 9:eadi0204. [PMID: 37878707 PMCID: PMC10599611 DOI: 10.1126/sciadv.adi0204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023]
Abstract
Quantum advantage in solving physical problems is still hard to assess due to hardware limitations. However, algorithms designed for quantum computers may engender transformative frameworks for modeling and simulating paradigmatically hard systems. Here, we show that the quadratic unconstrained binary optimization encoding enables tackling classical many-body systems that are challenging for conventional Monte Carlo. Specifically, in self-assembled melts of rigid lattice ring polymers, the combination of high density, chain stiffness, and topological constraints results in divergent autocorrelation times for real-space Monte Carlo. Our quantum-inspired encoding overcomes this problem and enables sampling melts of lattice rings with fixed curvature and compactness, unveiling counterintuitive topological effects. Tackling the same problems with the D-Wave quantum annealer leads to substantial performance improvements and advantageous scaling of sampling computational cost with the size of the self-assembled ring melts.
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Affiliation(s)
- Francesco Slongo
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, I-34136 Trieste, Italy
| | - Philipp Hauke
- Pitaevskii BEC Center, Department of Physics, University of Trento, Via Sommarive 14, I-38123 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, I-38123 Povo, Trento, Italy
| | - Pietro Faccioli
- Department of Physics and BiQuTe Center, University of Milano-Bicocca, Piazza della Scienza 3, I-20126 Milan, Italy
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Povo, Trento, Italy
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, I-34136 Trieste, Italy
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2
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McDonald J, von Spakovsky MR, Reynolds WT. Predicting non-equilibrium folding behavior of polymer chains using the steepest-entropy-ascent quantum thermodynamic framework. J Chem Phys 2023; 158:104904. [PMID: 36922120 DOI: 10.1063/5.0137444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
The steepest-entropy-ascent quantum thermodynamic (SEAQT) framework is used to explore the influence of heating and cooling on polymer chain folding kinetics. The framework predicts how a chain moves from an initial non-equilibrium state to stable equilibrium along a unique thermodynamic path. The thermodynamic state is expressed by occupation probabilities corresponding to the levels of a discrete energy landscape. The landscape is generated using the Replica Exchange Wang-Landau method applied to a polymer chain represented by a sequence of hydrophobic and polar monomers with a simple hydrophobic-polar amino acid model. The chain conformation evolves as energy shifts among the levels of the energy landscape according to the principle of steepest entropy ascent. This principle is implemented via the SEAQT equation of motion. The SEAQT framework has the benefit of providing insight into structural properties under non-equilibrium conditions. Chain conformations during heating and cooling change continuously without sharp transitions in morphology. The changes are more drastic along non-equilibrium paths than along quasi-equilibrium paths. The SEAQT-predicted kinetics are fitted to rates associated with the experimental intensity profiles of cytochrome c protein folding with Rouse dynamics.
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Affiliation(s)
- Jared McDonald
- Materials Science and Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, USA
| | | | - William T Reynolds
- Materials Science and Engineering Department, Virginia Tech, Blacksburg, Virginia 24061, USA
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3
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Wilson MS, Landau DP. Thermodynamics of hydrophobic-polar model proteins on the face-centered cubic lattice. Phys Rev E 2021; 104:025303. [PMID: 34525583 DOI: 10.1103/physreve.104.025303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
The HP model, a coarse-grained protein representation with only hydrophobic (H) and polar (P) amino acids, has already been extensively studied on the simple cubic (SC) lattice. However, this geometry severely restricts possible bond angles, and a simple improvement is to instead use the face-centered cubic (fcc) lattice. In this paper, the density of states and ground state energies are calculated for several benchmark HP sequences on the fcc lattice using the replica-exchange Wang-Landau algorithm and a powerful set of Monte Carlo trial moves. Results from the fcc lattice proteins are directly compared with those obtained from a previous lattice protein folding study with a similar methodology on the SC lattice. A thermodynamic analysis shows comparable folding behavior between the two lattice geometries, but with a greater rate of hydrophobic-core formation persisting into lower temperatures on the fcc lattice.
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Affiliation(s)
- Matthew S Wilson
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| | - David P Landau
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
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4
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Farris ACK, Seaton DT, Landau DP. Effects of lattice constraints in coarse-grained protein models. J Chem Phys 2021; 154:084903. [PMID: 33639740 DOI: 10.1063/5.0038184] [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
We compare and contrast folding behavior in several coarse-grained protein models, both on- and off-lattice, in an attempt to uncover the effect of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods-Wang-Landau sampling, multicanonical sampling, replica-exchange Wang-Landau sampling, and replica-exchange multicanonical sampling, we investigate the thermodynamic and structural behavior of the protein Crambin within the context of the hydrophobic-polar, hydrophobic-"neutral"-polar (H0P), and semi-flexible H0P model frameworks. We uncover the folding process in all cases; all models undergo, at least, the two major structural transitions observed in nature-the coil-globule collapse and the folding transition. As the complexity of the model increases, these two major transitions begin to split into multi-step processes, wherein the lattice coarse-graining has a significant impact on the details of these processes. The results show that the level of structural coarse-graining is coupled to the level of interaction coarse-graining.
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Affiliation(s)
- Alfred C K Farris
- Department of Physics and Astronomy, Oxford College of Emory University, Oxford, Georgia 30054, USA
| | - Daniel T Seaton
- Open Learning, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David P Landau
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
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5
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Miermans CA, Broedersz CP. A lattice kinetic Monte-Carlo method for simulating chromosomal dynamics and other (non-)equilibrium bio-assemblies. SOFT MATTER 2020; 16:544-556. [PMID: 31808764 DOI: 10.1039/c9sm01835b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biological assemblies in living cells such as chromosomes constitute large many-body systems that operate in a fluctuating, out-of-equilibrium environment. Since a brute-force simulation of that many degrees of freedom is currently computationally unfeasible, it is necessary to perform coarse-grained stochastic simulations. Here, we develop all tools necessary to write a lattice kinetic Monte-Carlo (LKMC) algorithm capable of performing such simulations. We discuss the validity and limits of this approach by testing the results of the simulation method in simple settings. Importantly, we illustrate how at large external forces Metropolis-Hastings kinetics violate the fluctuation-dissipation and steady-state fluctuation theorems and discuss better alternatives. Although this simulation framework is rather general, we demonstrate our approach using a DNA polymer with interacting SMC condensin loop-extruding enzymes. Specifically, we show that the scaling behavior of the loop-size distributions that we obtain in our LKMC simulations of this SMC-DNA system is consistent with that reported in other studies using Brownian dynamics simulations and analytic approaches. Moreover, we find that the irreversible dynamics of these enzymes under certain conditions result in frozen, sterically jammed polymer configurations, highlighting a potential pitfall of this approach.
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Affiliation(s)
- Christiaan A Miermans
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
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Farris ACK, Shi G, Wüst T, Landau DP. The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study. J Chem Phys 2018; 149:125101. [PMID: 30278675 DOI: 10.1063/1.5045482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using Monte Carlo simulations, we investigate simple, physically motivated extensions to the hydrophobic-polar lattice protein model for the small (46 amino acid) protein Crambin. We use two-dimensional replica-exchange Wang-Landau sampling to study the effects of a bond angle stiffness parameter on the folding and uncover a new step in the collapse process for particular values of this stiffness parameter. A physical interpretation of the folding is developed by analysis of changes in structural quantities, and the free energy landscape is explored. For these special values of stiffness, we find non-degenerate ground states, a property that is consistent with behavior of real proteins, and we use these unique ground states to elucidate the formation of native contacts during the folding process. Through this analysis, we conclude that chain-stiffness is particularly influential in the low energy, low temperature regime of the folding process once the lattice protein has partially collapsed.
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Affiliation(s)
- Alfred C K Farris
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| | - Guangjie Shi
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| | - Thomas Wüst
- Scientific IT Services, ETH Zürich, 8092 Zürich, Switzerland
| | - David P Landau
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
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7
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Wilson MS, Shi G, Wüst T, Li YW, Landau DP. Influence of substrate pattern on the adsorption of HP lattice proteins. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1471691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Matthew S. Wilson
- Centre for Simulational Physics, The University of Georgia, Athens, GA, USA
| | - Guangjie Shi
- Centre for Simulational Physics, The University of Georgia, Athens, GA, USA
| | - Thomas Wüst
- Scientific IT Services, ETH Zürich IT Services, Zürich, Switzerland
| | - Ying Wai Li
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David P. Landau
- Centre for Simulational Physics, The University of Georgia, Athens, GA, USA
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8
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Affiliation(s)
- Yani Zhao
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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9
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Wüst T, Reith D, Virnau P. Sequence determines degree of knottedness in a coarse-grained protein model. PHYSICAL REVIEW LETTERS 2015; 114:028102. [PMID: 25635563 DOI: 10.1103/physrevlett.114.028102] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Indexed: 06/04/2023]
Abstract
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar lattice protein model. By employing large-scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.
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Affiliation(s)
- Thomas Wüst
- Scientific IT Services, ETH Zürich, 8092 Zürich, Switzerland
| | - Daniel Reith
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Peter Virnau
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128 Mainz, Germany
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10
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Shi G, Vogel T, Wüst T, Li YW, Landau DP. Effect of single-site mutations on hydrophobic-polar lattice proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:033307. [PMID: 25314564 DOI: 10.1103/physreve.90.033307] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 06/04/2023]
Abstract
We developed a heuristic method for determining the ground-state degeneracy of hydrophobic-polar (HP) lattice proteins, based on Wang-Landau and multicanonical sampling. It is applied during comprehensive studies of single-site mutations in specific HP proteins with different sequences. The effects in which we are interested include structural changes in ground states, changes of ground-state energy, degeneracy, and thermodynamic properties of the system. With respect to mutations, both extremely sensitive and insensitive positions in the HP sequence have been found. That is, ground-state energies and degeneracies, as well as other thermodynamic and structural quantities, may be either largely unaffected or may change significantly due to mutation.
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Affiliation(s)
- Guangjie Shi
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| | - Thomas Vogel
- Theoretical Division (T-1), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Thomas Wüst
- Scientific IT Services, ETH Zürich IT Services, 8092 Zürich, Switzerland
| | - Ying Wai Li
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - David P Landau
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
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11
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Vogel T, Li YW, Wüst T, Landau DP. Scalable replica-exchange framework for Wang-Landau sampling. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:023302. [PMID: 25215846 DOI: 10.1103/physreve.90.023302] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Indexed: 06/03/2023]
Abstract
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.
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Affiliation(s)
- Thomas Vogel
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| | - Ying Wai Li
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Thomas Wüst
- Scientific IT Services, ETH Zürich IT Services, 8092 Zürich, Switzerland
| | - David P Landau
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
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12
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Dasmahapatra AK, Sanka VM. Conformational transition of H-shaped branched polymers. J Chem Phys 2014; 140:094904. [DOI: 10.1063/1.4867055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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13
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Li Y, Wüst T, Landau D. Wang–Landau sampling of the interplay between surface adsorption and folding of HP lattice proteins. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.847273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Pattanasiri B, Li YW, Landau DP, Wüst T, Triampo W. Thermodynamics and structural properties of a confined HP protein determined by Wang-Landau simulation. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/454/1/012071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Li YW, Wüst T, Landau DP. Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:012706. [PMID: 23410358 DOI: 10.1103/physreve.87.012706] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 10/12/2012] [Indexed: 06/01/2023]
Abstract
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are considered with different types of surfaces, each of which attract either all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. The diversity of folding behavior in dependence of surface strength is discussed. Analyzing the combined patterns of various structural observables, such as, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, we are able to identify generic categories of folding and transition hierarchies. We also infer a connection between these transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the interchain attraction among H monomers. The validity of our proposed classification scheme is reinforced by the analysis of additional benchmark sequences. We thus believe that the folding hierarchies and identification scheme are generic for HP proteins interacting with attractive surfaces, regardless of chain length, sequence, or surface attraction.
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Affiliation(s)
- Ying Wai Li
- Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, USA.
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16
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Pattanasiri B, Li YW, Landau DP, Wüst T, Triampo W. Conformational transitions of a confined lattice protein: A Wang-Landau study. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/402/1/012048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Györffy D, Závodszky P, Szilágyi A. "Pull moves" for rectangular lattice polymer models are not fully reversible. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:1847-1849. [PMID: 23221093 DOI: 10.1109/tcbb.2012.129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
"Pull moves" is a popular move set for lattice polymer model simulations. We show that the proof given for its reversibility earlier is flawed, and some moves are irreversible, which leads to biases in the parameters estimated from the simulations. We show how to make the move set fully reversible.
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Affiliation(s)
- Dániel Györffy
- Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Karolina ut 29, H-1113 Budapest, Hungary.
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18
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Tang W, Zhou Q. Finding multiple minimum-energy conformations of the hydrophobic-polar protein model via multidomain sampling. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:031909. [PMID: 23030946 DOI: 10.1103/physreve.86.031909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Indexed: 06/01/2023]
Abstract
We demonstrate the efficiency of the multidomain sampler (MDS) in finding multiple distinct global minima and low-energy local minima in the hydrophobic-polar (HP) lattice protein model. Extending the idea of partitioning energy space in the Wang-Landau algorithm, our approach introduces an additional partitioning scheme to divide the protein conformation space into local basins of attraction. This double-partitioning design is very powerful in guiding the sampler to visit the basins of unexplored local minima. An H-residue subchain distance is used to merge the basins of similar local minima into one domain, which increases the diversity among identified minimum-energy conformations. Moreover, a visit-enhancement factor is introduced for long protein chains to facilitate jumps between basins. Results on three benchmark protein sequences reveal that our approach is capable of finding multiple global minima and hundreds of low-energy local minima of great diversity.
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Affiliation(s)
- Wei Tang
- Department of Materials Science and Engineering, University of California, Los Angeles, California 90095, USA
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Wüst T, Landau DP. Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins. J Chem Phys 2012; 137:064903. [DOI: 10.1063/1.4742969] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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20
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Radhakrishna M, Sharma S, Kumar SK. Enhanced Wang Landau sampling of adsorbed protein conformations. J Chem Phys 2012; 136:114114. [DOI: 10.1063/1.3691669] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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21
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Li YW, Wüst T, Landau DP. Monte Carlo simulations of the HP model (the "Ising model" of protein folding). COMPUTER PHYSICS COMMUNICATIONS 2011; 182:1896-1899. [PMID: 21804642 PMCID: PMC3143505 DOI: 10.1016/j.cpc.2010.12.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and are largely inaccessible to "standard" Monte Carlo methods.
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Affiliation(s)
- Ying Wai Li
- Center for Simulational Physics, The University of Georgia, Athens, GA 30602, U.S.A
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22
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Wüst T, Landau DP. Versatile approach to access the low temperature thermodynamics of lattice polymers and proteins. PHYSICAL REVIEW LETTERS 2009; 102:178101. [PMID: 19518836 DOI: 10.1103/physrevlett.102.178101] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Indexed: 05/27/2023]
Abstract
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and the interacting self-avoiding walk (ISAW) model for homopolymers. We obtain accurate estimates of thermodynamic quantities for HP sequences with >100 monomers and for ISAWs up to >500 monomers. Our procedure possesses an intrinsic simplicity and overcomes the limitations inherent in more tailored approaches making it interesting for a broad range of protein and polymer models.
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Affiliation(s)
- Thomas Wüst
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA.
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23
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Hsu HP, Mehra V, Nadler W, Grassberger P. Growth-based optimization algorithm for lattice heteropolymers. ACTA ACUST UNITED AC 2003; 68:021113. [PMID: 14524959 DOI: 10.1103/physreve.68.021113] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2002] [Indexed: 11/07/2022]
Abstract
An improved version of the pruned-enriched-Rosenbluth method (PERM) is proposed and tested on finding lowest energy states in simple models of lattice heteropolymers. It is found to outperform not only the previous version of PERM, but also all other fully blind general purpose stochastic algorithms which have been employed on this problem. In many cases, it found new lowest energy states missed in previous papers. Limitations are discussed.
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Affiliation(s)
- Hsiao-Ping Hsu
- John-von-Neumann Institute for Computing, Forschungszentrum Jülich, D-52425 Jülich, Germany
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24
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Hsu HP, Mehra V, Nadler W, Grassberger P. Growth algorithms for lattice heteropolymers at low temperatures. J Chem Phys 2003. [DOI: 10.1063/1.1522710] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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26
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27
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Tschöp W, Noolandi J. Real-space renormalization group technique for low-lying energy states in chain folding. J Chem Phys 1998. [DOI: 10.1063/1.477241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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30
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Doye JPK, Sear RP, Frenkel D. The effect of chain stiffness on the phase behaviour of isolated homopolymers. J Chem Phys 1998. [DOI: 10.1063/1.475592] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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