pith. sign in

arxiv: 2606.19418 · v1 · pith:JFFPWMLEnew · submitted 2026-06-17 · ❄️ cond-mat.soft · physics.chem-ph

Sequential replica exchange with solute tempering for atomistic modeling of supramolecular polymer structures

Hadi H. Arefi , Takeshi Yamamoto This is my paper

Pith reviewed 2026-06-26 19:07 UTC · model grok-4.3

classification ❄️ cond-mat.soft physics.chem-ph
keywords supramolecular polymersreplica exchange with solute temperingsequential constructionmolecular dynamicshydrogen bondingself-assemblyatomistic simulation
0
0 comments X

The pith

Sequential addition of monomers with targeted REST generates correct H-bonding patterns in supramolecular polymers at lower cost than global tempering.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper proposes building supramolecular polymer structures by adding monomers one at a time rather than tempering the entire assembly at once. For each new monomer, replica exchange with solute tempering is applied only to that monomer to locate its optimal binding site using an energy-based score. The process repeats until the desired chain length is reached, under the assumption that growth occurs as a one-dimensional polymer. Tests on a model system in explicit solvent show that the resulting structures display the expected hydrogen-bonding patterns while requiring fewer replicas overall and allowing replicas to traverse the ladder more efficiently. The method is presented as a practical alternative when full global REST becomes computationally prohibitive due to system size or order-disorder transitions.

Core claim

By constructing the polymer through repeated cycles of monomer addition followed by REST applied selectively to the incoming monomer, the method locates binding sites that yield characteristic H-bonding patterns, all while using fewer replicas and achieving faster traversal across the replica ladder than global REST on the entire assembly.

What carries the argument

The sequential REST procedure, in which each new monomer is added to an existing chain and REST is applied only to that monomer to identify its optimal binding position via an energy-based scoring function.

If this is right

  • The procedure generates a polymer structure with characteristic H-bonding patterns.
  • It does so at reduced computational costs compared with global REST.
  • Replica traversal efficiency improves significantly.
  • The approach becomes usable for modeling supramolecular polymers in cases where global REST simulations are too demanding.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • The method's replica scaling may remain favorable even as chain length increases beyond the tested model.
  • The energy scoring step could be replaced by other selection criteria without changing the overall sequential framework.
  • The assumption of one-dimensional growth limits direct application to branched or two-dimensional assemblies unless the procedure is extended.

Load-bearing premise

Polymerization occurs strictly in one dimension by sequential addition of new monomers to an existing chain.

What would settle it

A side-by-side run on the same model system in which the sequential procedure produces structures lacking the characteristic H-bonding patterns or higher in energy than those obtained from a converged global REST simulation.

Figures

Figures reproduced from arXiv: 2606.19418 by Hadi H. Arefi, Takeshi Yamamoto.

Figure 1
Figure 1. Figure 1: FIG. 1. Structure of benzene-1,3,5-tricarboxyamide (BTA) [PITH_FULL_IMAGE:figures/full_fig_p003_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: displays the evolution of Lp that monitors the length of the longest supramolecular polymer formed in the system. This figure shows that the system with FIG. 2. Evolution of the polymer length Lp(t) obtained from cMD simulations for systems with 5, 10, 15, and 20 monomers. Typical self-assembled structures are also depicted. cMD does not produce a fully elongated polymer (except for the 5-mer case) because… view at source ↗
Figure 3
Figure 3. Figure 3: FIG. 3. Evolution of the polymer length ( [PITH_FULL_IMAGE:figures/full_fig_p005_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: FIG. 4. Replica traversal in temperature space obtained from [PITH_FULL_IMAGE:figures/full_fig_p006_4.png] view at source ↗
Figure 6
Figure 6. Figure 6: FIG. 6. Evolution of the polymer length ( [PITH_FULL_IMAGE:figures/full_fig_p007_6.png] view at source ↗
Figure 7
Figure 7. Figure 7: FIG. 7. Schematic illustration of the sequential REST ap [PITH_FULL_IMAGE:figures/full_fig_p008_7.png] view at source ↗
Figure 8
Figure 8. Figure 8: FIG. 8. (a) Monomer-aggregate interaction energy [PITH_FULL_IMAGE:figures/full_fig_p009_8.png] view at source ↗
Figure 9
Figure 9. Figure 9: FIG. 9. Typical polymer structures obtained from sequential [PITH_FULL_IMAGE:figures/full_fig_p010_9.png] view at source ↗
read the original abstract

Predicting detailed atomistic structures of self-assembling systems remains a challenge for all-atom molecular dynamics simulations. Replica exchange with solute tempering (REST) has been used to study those systems by accelerating all monomers in a global and uniform manner. While such a global approach can in principle predict any morphology of the system, it has computational drawbacks such as inefficient replica traversal due to order-disorder transitions and the growing number of replicas with system size. To address these issues, here we propose an alternative, stepwise construction approach to modeling supramolecular polymers under the assumption of one-dimensional polymerization. Specifically, we generate polymer structures by adding new monomers one by one to the system and applying REST to the new monomers to find their optimal binding positions based on an energy-based scoring function. The monomer addition and enhanced sampling are repeated sequentially until a polymer of desired length is obtained. We test the above procedure using a model supramolecular polymer in explicit solvent, and show that it can generate a polymer structure with characteristic H-bonding patterns at reduced computational costs, while also improving the efficiency of replica traversal significantly. We thus expect that the sequential REST will be useful for modeling supramolecular polymers, particularly for cases where global REST simulations are too demanding computationally.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 1 minor

Summary. The manuscript proposes a sequential replica exchange with solute tempering (REST) procedure for atomistic modeling of supramolecular polymers. Under the assumption of one-dimensional polymerization, new monomers are added sequentially to an existing chain and REST is applied only to the newly added monomer(s) to optimize binding positions via an energy-based score; the process repeats until the target length is reached. The authors test the method on a model supramolecular polymer in explicit solvent and claim that it generates structures exhibiting characteristic H-bonding patterns at reduced computational cost while also improving replica traversal efficiency relative to global REST.

Significance. If the sequential construction reliably yields correct global structures, the approach could offer a practical route to modeling larger supramolecular assemblies where the replica count and sampling inefficiencies of global REST become prohibitive. The method directly targets the scaling limitations noted in the abstract. However, the significance is limited by the absence of quantitative validation metrics and controls addressing the irreversibility of early monomer placements.

major comments (2)
  1. [Abstract / Method] Abstract and method description: the procedure applies REST exclusively to newly added monomers while fixing prior monomers in place. This renders the one-dimensional polymerization assumption load-bearing for structural correctness, because any early local minimum in binding geometry cannot be revised even if cooperative H-bonding across multiple monomers would favor a different arrangement. No indication is given that earlier monomers are re-sampled in later stages, nor is a control that relaxes the completed chain reported.
  2. [Abstract / Results] Results / Validation: the claim that the procedure 'can generate a polymer structure with characteristic H-bonding patterns' is presented without quantitative metrics (e.g., H-bond occupancy fractions, RMSD to reference structures, or energy distributions), error bars, comparison to global REST or unbiased MD baselines, or the number of independent runs performed. The abstract supplies only a qualitative statement, which is insufficient to substantiate the headline performance claims.
minor comments (1)
  1. [Abstract] The statement that replica traversal efficiency is 'improved significantly' lacks any numerical support (e.g., round-trip times, acceptance rates, or diffusion constants) in the abstract.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for their thorough review and constructive feedback on our manuscript. We address the major comments point by point below and indicate where revisions will be made to improve the clarity and substantiation of our claims.

read point-by-point responses

  1. Referee: [Abstract / Method] Abstract and method description: the procedure applies REST exclusively to newly added monomers while fixing prior monomers in place. This renders the one-dimensional polymerization assumption load-bearing for structural correctness, because any early local minimum in binding geometry cannot be revised even if cooperative H-bonding across multiple monomers would favor a different arrangement. No indication is given that earlier monomers are re-sampled in later stages, nor is a control that relaxes the completed chain reported.

    Authors: We agree that the sequential REST method relies on the one-dimensional polymerization assumption, which is stated in the manuscript title and abstract. Under this assumption, early monomer placements are not revised in subsequent steps, as the focus is on efficient construction for systems where 1D growth is appropriate. We will revise the method description to explicitly note this limitation and the absence of re-sampling for prior monomers. A control relaxing the full chain was not performed in the current study, as it would defeat the purpose of the sequential approach for computational efficiency; however, we can add a discussion on this point. revision: partial

  2. Referee: [Abstract / Results] Results / Validation: the claim that the procedure 'can generate a polymer structure with characteristic H-bonding patterns' is presented without quantitative metrics (e.g., H-bond occupancy fractions, RMSD to reference structures, or energy distributions), error bars, comparison to global REST or unbiased MD baselines, or the number of independent runs performed. The abstract supplies only a qualitative statement, which is insufficient to substantiate the headline performance claims.

    Authors: The full manuscript includes figures demonstrating the H-bonding patterns and replica traversal efficiency. To address the concern, we will revise the abstract and results section to include quantitative metrics such as H-bond occupancy fractions, comparisons to global REST, and details on the number of independent simulations performed, along with error bars where applicable. This will provide stronger substantiation for the performance claims. revision: yes

Circularity Check

0 steps flagged

No circularity: new sequential procedure tested on external model system

full rationale

The paper proposes a stepwise monomer-addition procedure under an explicit one-dimensional polymerization assumption and reports observed performance gains on a model supramolecular polymer in explicit solvent. No equations, fitted parameters, or self-citations are invoked that reduce any claimed result to an input by construction; the central claims rest on direct simulation outcomes rather than tautological re-labeling or self-referential fitting. The derivation chain is therefore self-contained against external benchmarks.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

The central claim rests on the domain assumption of strictly one-dimensional growth and on the unstated details of the energy-based scoring function used to accept new monomers; no free parameters or invented entities are introduced in the abstract.

axioms (1)
  • domain assumption One-dimensional polymerization
    The stepwise addition procedure is defined only under this assumption; if growth occurs in multiple dimensions the sequential construction no longer applies.

pith-pipeline@v0.9.1-grok · 5752 in / 1210 out tokens · 19555 ms · 2026-06-26T19:07:16.756864+00:00 · methodology

discussion (0)

Sign in with ORCID, Apple, or X to comment. Anyone can read and Pith papers without signing in.

Reference graph

Works this paper leans on

79 extracted references

  1. [1]

    and Yamamoto, Takeshi , journal =

    Arefi, Hadi H. and Yamamoto, Takeshi , journal =. Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering , year =

  2. [2]

    Self-Assembly of Nanocubic Molecular Capsules via Solvent-Guided Formation of Rectangular Blocks , year =

    Yamamoto, Takeshi and Arefi, Hadi and Shanker, Sudhanshu and Sato, Hirofumi and Hiraoka, Shuichi , journal =. Self-Assembly of Nanocubic Molecular Capsules via Solvent-Guided Formation of Rectangular Blocks , year =

  3. [3]

    and Boncheva, Mila , journal =

    Whitesides, George M. and Boncheva, Mila , journal =. Beyond molecules: Self-assembly of mesoscopic and macroscopic components , year =

  4. [4]

    Toward complex matter: Supramolecular chemistry and self-organization , year =

    Lehn, Jean-Marie , journal =. Toward complex matter: Supramolecular chemistry and self-organization , year =

  5. [5]

    Designing the Molecular World: Chemistry at the Frontier , year =

    Ball, Philip , publisher =. Designing the Molecular World: Chemistry at the Frontier , year =

  6. [6]

    and Folmer, B

    Brunsveld, L. and Folmer, B. J. B. and Meijer, E. W. and Sijbesma, R. P. , journal =. Supramolecular Polymers , year =

  7. [7]

    Jonkheijm, Pascal and van der Schoot, Paul and Schenning, Albertus P. H. J. and Meijer, E. W. , journal =. Probing the Solvent-Assisted Nucleation Pathway in Chemical Self-Assembly , year =

  8. [8]

    and Schaefer, Charley and de Greef, Tom F

    Korevaar, Peter A. and Schaefer, Charley and de Greef, Tom F. A. and Meijer, E. W. , journal =. Controlling Chemical Self-Assembly by Solvent-Dependent Dynamics , year =

  9. [9]

    and Melo, Marcelo C.R

    Bernardi, Rafael C. and Melo, Marcelo C.R. and Schulten, Klaus , journal =. Enhanced sampling techniques in molecular dynamics simulations of biological systems , year =

  10. [10]

    Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides — The Alanine Dipeptide Case Study , year =

    Vymětal, Jiří and Vondrášek, Jiří , journal =. Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides — The Alanine Dipeptide Case Study , year =

  11. [11]

    2011 , issn =

    Cooperativity in the stacking of benzene-1,3,5-tricarboxamide: The role of dispersion , journal =. 2011 , issn =

    2011

  12. [12]

    and Fiorin, Giacomo and Klein, Michael L

    Bejagam, Karteek K. and Fiorin, Giacomo and Klein, Michael L. and Balasubramanian, Sundaram , journal =. Supramolecular Polymerization of Benzene-1,3,5-tricarboxamide: A Molecular Dynamics Simulation Study , year =

  13. [13]

    and Balasubramanian, Sundaram , journal =

    Bejagam, Karteek K. and Balasubramanian, Sundaram , journal =. Supramolecular Polymerization: A Coarse Grained Molecular Dynamics Study , year =

  14. [14]

    and Kulkarni, Chidambar and George, Subi J

    Bejagam, Karteek K. and Kulkarni, Chidambar and George, Subi J. and Balasubramanian, Sundaram , journal =. External electric field reverses helical handedness of a supramolecular columnar stack , year =

  15. [15]

    and Remsing, Richard C

    Bejagam, Karteek K. and Remsing, Richard C. and Klein, Michael L. and Balasubramanian, Sundaram , journal =. Understanding the self-assembly of amino ester-based benzene-1,3,5-tricarboxamides using molecular dynamics simulations , year =

  16. [16]

    , journal =

    Kulkarni, Chidambar and Balasubramanian, Sundaram and George, Subi J. , journal =. What Molecular Features Govern the Mechanism of Supramolecular Polymerization? , year =

  17. [17]

    Cantekin, Seda and de Greef, Tom F. A. and Palmans, Anja R. A. , journal =. Benzene-1,3,5-tricarboxamide: a versatile ordering moiety for supramolecular chemistry , year =

  18. [18]

    , title =

    Kim, Jaegil and Keyes, Thomas and Straub, John E. , title =. J. Chem. Phys. , volume =. 2010 , month =

    2010

  19. [19]

    de Greef, Tom F. A. and Meijer, E. W. , journal =. Supramolecular polymers , year =

  20. [20]

    De Greef, Tom F. A. and Smulders, Maarten M. J. and Wolffs, Martin and Schenning, Albert P. H. J. and Sijbesma, Rint P. and Meijer, E. W. , journal =. Supramolecular Polymerization , year =

  21. [21]

    and Meijer, E

    Aida, T. and Meijer, E. W. and Stupp, S. I. , journal =. Functional Supramolecular Polymers , year =

  22. [22]

    Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration , year =

    Abrams, Cameron and Bussi, Giovanni , journal =. Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration , year =

  23. [23]

    and Martiniani, Stefano and Stevenson, Jacob D

    Ballard, Andrew J. and Martiniani, Stefano and Stevenson, Jacob D. and Somani, Sandeep and Wales, David J. , journal =. Exploiting the potential energy landscape to sample free energy , year =

  24. [24]

    , journal =

    Hansmann, Ulrich H.E. , journal =. Parallel tempering algorithm for conformational studies of biological molecules , year =

  25. [25]

    Replica-exchange molecular dynamics method for protein folding , year =

    Sugita, Yuji and Okamoto, Yuko , journal =. Replica-exchange molecular dynamics method for protein folding , year =

  26. [26]

    2000 , issn =

    Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape , journal =. 2000 , issn =

    2000

  27. [27]

    Jung, Jaewoon and Kobayashi, Chigusa and Sugita, Yuji , title =. J. Comput. Chem. , volume =

  28. [28]

    Kamiya, Motoshi and Sugita, Yuji , title =. J. Chem. Phys. , volume =. 2018 , month =

    2018

  29. [29]

    Gnanakaran and Angel E

    Hugh Nymeyer and S. Gnanakaran and Angel E. García , title =. Numerical Computer Methods, Part D , series =. 2004 , publisher =

    2004

  30. [30]

    and Berne, B

    Liu, Pu and Kim, Byungchan and Friesner, Richard A. and Berne, B. J. , journal =. Replica exchange with solute tempering: A method for sampling biological systems in explicit water , year =

  31. [31]

    and Zhou, Ruhong and Berne, B

    Huang, Xuhui and Hagen, Morten and Kim, Byungchan and Friesner, Richard A. and Zhou, Ruhong and Berne, B. J. , journal =. Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems , year =

  32. [32]

    and Berne, B

    Wang, Lingle and Friesner, Richard A. and Berne, B. J. , journal =. Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2) , year =

  33. [33]

    On easy implementation of a variant of the replica exchange with solute tempering in GROMACS , year =

    Terakawa, Tsuyoshi and Kameda, Tomoshi and Takada, Shoji , journal =. On easy implementation of a variant of the replica exchange with solute tempering in GROMACS , year =

  34. [34]

    Hamiltonian replica exchange in GROMACS: a flexible implementation , year =

    Bussi, Giovanni , journal =. Hamiltonian replica exchange in GROMACS: a flexible implementation , year =

  35. [35]

    , journal =

    Camilloni, Carlo and Provasi, Davide and Tiana, Guido and Broglia, Ricardo A. , journal =. Exploring the protein G helix free‐energy surface by solute tempering metadynamics , year =

  36. [36]

    and Walsh, Tiffany R

    Wright, Louise B. and Walsh, Tiffany R. , journal =. Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide , year =

  37. [37]

    and Wu, Yujie and Kim, Byungchan and Sherman, Woody and Shelley, John C

    Wang, Lingle and Deng, Yuqing and Knight, Jennifer L. and Wu, Yujie and Kim, Byungchan and Sherman, Woody and Shelley, John C. and Lin, Teng and Abel, Robert , journal =. Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors , year =

  38. [38]

    , journal =

    Huang, Kun and García, Angel E. , journal =. Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering , year =

  39. [39]

    and Tirado-Rives, Julian and Jorgensen, William L

    Cole, Daniel J. and Tirado-Rives, Julian and Jorgensen, William L. , journal =. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering , year =

  40. [40]

    Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent , year =

    Stirnemann, Guillaume and Sterpone, Fabio , journal =. Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent , year =

  41. [41]

    Disorder-to-Order Transition of an Active-Site Loop Mediates the Allosteric Activation of Sortase A , year =

    Pang, Xiaodong and Zhou, Huan-Xiang , journal =. Disorder-to-Order Transition of an Active-Site Loop Mediates the Allosteric Activation of Sortase A , year =

  42. [42]

    and Lockhart, Christopher and Klimov, Dmitri K

    Smith, Amy K. and Lockhart, Christopher and Klimov, Dmitri K. , journal =. Does Replica Exchange with Solute Tempering Efficiently Sample Aβ Peptide Conformational Ensembles? , year =

  43. [43]

    and Leenders, Christianus M

    Garzoni, Matteo and Baker, Matthew B. and Leenders, Christianus M. A. and Voets, Ilja K. and Albertazzi, Lorenzo and Palmans, Anja R. A. and Meijer, E. W. and Pavan, Giovanni M. , journal =. Effect of H-Bonding on Order Amplification in the Growth of a Supramolecular Polymer in Water , year =

  44. [44]

    , journal =

    Bochicchio, Davide and Pavan, Giovanni M. , journal =. From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations , year =

  45. [45]

    , journal =

    Bochicchio, Davide and Pavan, Giovanni M. , journal =. Effect of Concentration on the Supramolecular Polymerization Mechanism via Implicit-Solvent Coarse-Grained Simulations of Water-Soluble 1,3,5-Benzenetricarboxamide , year =

  46. [46]

    Filot, Ivo A. W. and Palmans, Anja R. A. and Hilbers, Peter A. J. and van Santen, Rutger A. and Pidko, Evgeny A. and de Greef, Tom F. A. , journal =. Understanding Cooperativity in Hydrogen-Bond-Induced Supramolecular Polymerization: A Density Functional Theory Study , year =

  47. [47]

    Replica exchange with guided annealing for accelerated sampling of disordered protein conformations , year =

    Zhang, Weihong and Chen, Jianhan , journal =. Replica exchange with guided annealing for accelerated sampling of disordered protein conformations , year =

  48. [48]

    A temperature predictor for parallel tempering simulations , year =

    Patriksson, Alexandra and van der Spoel, David , journal =. A temperature predictor for parallel tempering simulations , year =

  49. [49]

    Frederix, Pim W. J. M. and Patmanidis, Ilias and Marrink, Siewert J. , journal =. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments , year =

  50. [50]

    , journal =

    Bochicchio, Davide and Pavan, Giovanni M. , journal =. Molecular modelling of supramolecular polymers , year =

  51. [51]

    and Balasubramanian, S

    Korlepara, Divya B. and Balasubramanian, S. , journal =. Molecular modelling of supramolecular one dimensional polymers , year =

  52. [52]

    Living supramolecular polymerization realized through a biomimetic approach , year =

    Ogi, Soichiro and Sugiyasu, Kazunori and Manna, Swarup and Samitsu, Sadaki and Takeuchi, Masayuki , journal =. Living supramolecular polymerization realized through a biomimetic approach , year =

  53. [53]

    Impact of Alkyl Spacer Length on Aggregation Pathways in Kinetically Controlled Supramolecular Polymerization , year =

    Ogi, Soichiro and Stepanenko, Vladimir and Thein, Johannes and Würthner, Frank , journal =. Impact of Alkyl Spacer Length on Aggregation Pathways in Kinetically Controlled Supramolecular Polymerization , year =

  54. [54]

    Graphenes as Potential Material for Electronics , year =

    Wu, Jishan and Pisula, Wojciech and Müllen, Klaus , journal =. Graphenes as Potential Material for Electronics , year =

  55. [55]

    and Vijayakumar, Chakkooth , journal =

    Ajayaghosh, Ayyappanpillai and Praveen, Vakayil K. and Vijayakumar, Chakkooth , journal =. Organogels as scaffolds for excitation energy transfer and light harvesting , year =

  56. [56]

    Stimuli-responsive supramolecular polymeric materials , year =

    Yan, Xuzhou and Wang, Feng and Zheng, Bo and Huang, Feihe , journal =. Stimuli-responsive supramolecular polymeric materials , year =

  57. [57]

    and Guzman, Carmen X

    Peurifoy, Samuel R. and Guzman, Carmen X. and Braunschweig, Adam B. , journal =. Topology, assembly, and electronics: three pillars for designing supramolecular polymers with emergent optoelectronic behavior , year =

  58. [58]

    , journal =

    Herbst, Florian and Döhler, Diana and Michael, Philipp and Binder, Wolfgang H. , journal =. Self-Healing Polymers via Supramolecular Forces , year =

  59. [59]

    and de Vries, A

    Piskorz, Tomasz K. and de Vries, A. H. and van Esch, Jan H. , journal =. How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers , year =

  60. [60]

    Frederix, Pim W. J. M. and Idé, Julien and Altay, Yigit and Schaeffer, Gaël and Surin, Mathieu and Beljonne, David and Bondarenko, Anna S. and Jansen, Thomas L. C. and Otto, Sijbren and Marrink, Siewert J. , journal =. Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles , year =

  61. [61]

    and Monticelli, Luca and Melo, Manuel N

    Marrink, Siewert J. and Monticelli, Luca and Melo, Manuel N. and Alessandri, Riccardo and Tieleman, D. Peter and Souza, Paulo C. T. , journal =. Two decades of Martini: Better beads, broader scope , year =

  62. [62]

    and Schatz, George C

    Lai, Cheng-Tsung and Rosi, Nathaniel L. and Schatz, George C. , journal =. All-Atom Molecular Dynamics Simulations of Peptide Amphiphile Assemblies That Spontaneously Form Twisted and Helical Ribbon Structures , year =

  63. [63]

    and Schatz, George C

    Lee, One-Sun and Stupp, Samuel I. and Schatz, George C. , journal =. Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers , year =

  64. [64]

    Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] , year =

    Henin, Jerome and Lelievre, Tony and Shirts, Michael R and Valsson, Omar and Delemotte, Lucie , journal =. Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] , year =

  65. [65]

    Peptide Self-Assembled Nanocarriers for Cancer Drug Delivery , year =

    Kumar, Vijay Bhooshan and Ozguney, Busra and Vlachou, Anastasia and Chen, Yu and Gazit, Ehud and Tamamis, Phanourios , journal =. Peptide Self-Assembled Nanocarriers for Cancer Drug Delivery , year =

  66. [66]

    and Pan, Hongjun and Janesko, Benjamin G

    Capelli, Riccardo and Menke, Alexander J. and Pan, Hongjun and Janesko, Benjamin G. and Simanek, Eric E. and Pavan, Giovanni M. , journal =. Well-Tempered Metadynamics Simulations Predict the Structural and Dynamic Properties of a Chiral 24-Atom Macrocycle in Solution , year =

  67. [67]

    and Klimov, Dmitri K

    Smith, Amy K. and Klimov, Dmitri K. , journal =. De novo aggregation of Alzheimer’s Aβ25-35 peptides in a lipid bilayer , year =

  68. [68]

    and Tirado–Rives, Julian , journal =

    Jorgensen, William L. and Tirado–Rives, Julian , journal =. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO , year =

  69. [69]

    2008 , edition =

    Coarse-Graining of Condensed Phase and Biomolecular Systems , publisher =. 2008 , edition =

    2008

  70. [70]

    Circular dichroism of helical structures using semiempirical methods , year =

    Botek, Edith and Champagne, Benoît , journal =. Circular dichroism of helical structures using semiempirical methods , year =

  71. [71]

    and Harder, Edward and Lin, Teng and Abel, Robert and McCammon, J

    Kaus, Joseph W. and Harder, Edward and Lin, Teng and Abel, Robert and McCammon, J. Andrew and Wang, Lingle , journal =. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations , year =

  72. [72]

    and Greenwood, Jeremy and Romero, Donna L

    Wang, Lingle and Wu, Yujie and Deng, Yuqing and Kim, Byungchan and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shaughnessy and Dahlgren, Markus K. and Greenwood, Jeremy and Romero, Donna L. and Masse, Craig and Knight, Jennifer L. and Steinbrecher, Thomas and Beuming, Thijs and Damm, Wolfgang and Harder, Ed and Sherman, Woody and Brewe...

  73. [73]

    Eric and Jalalypour, Farzaneh and Johansson, Petter and Kutzner, Carsten and Łazarski, Grzegorz and Lemkul, Justin A

    Abraham, Mark and Alekseenko, Andrey and Andrews, Brian and Basov, Vladimir and Bauer, Paul and Bird, Hugh and Briand, Eliane and Brown, Ania and Doijade, Mahesh and Fiorin, Giacomo and Fleischmann, Stefan and Gorelov, Sergey and Gouaillardet, Gilles and Gray, Alan and Irrgang, M. Eric and Jalalypour, Farzaneh and Johansson, Petter and Kutzner, Carsten an...

    2025

  74. [74]

    , journal =

    Gasparotto, Piero and Bochicchio, Davide and Ceriotti, Michele and Pavan, Giovanni M. , journal =. Identifying and Tracking Defects in Dynamic Supramolecular Polymers , year =

  75. [75]

    On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction , year =

    Fukunishi, Hiroaki and Watanabe, Osamu and Takada, Shoji , journal =. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction , year =

  76. [76]

    Nymeyer and S

    H. Nymeyer and S. Gnanakaran and A. E. Garcia , Title =. Methods in Enzymology , Year =

  77. [77]

    Kim and T

    J. Kim and T. Keyes and J. E. Straub , Title =. J. Chem. Phys. , Year =

  78. [78]

    Jiang and H

    Y. Jiang and H. Zhang and Z. Cui and T. Tan , title =. J. Phys. Chem. Lett. , volume =

  79. [79]

    Borgis and S

    D. Borgis and S. Luukkonen and L. Belloni and G. Jeanmairet , title =. J. Chem. Phys. , volume =