23 papers · ranked by Valyu relevance
Yusuf Bugra Severoglu, Betul Yuksel, Cagatay Sucu, Nese Aral + 3 more
Solvents represent the quiet majority in biomolecular systems, yet modeling their influence with both speed and ri:gor remains a central challenge. This study maps the state of the art in implicit solvent theory and practice, spanning classical continuum electrostatics (PB/GB; DelPhi, APBS), modern nonpolar and…
Danil Kaliakin, Akhil Shajan, Fangchun Liang, Kenneth M. Merz Jr.
Sample-Based Quantum Diagonalization Authors: ['Danil Kaliakin' 'Akhil Shajan' 'Fangchun Liang' 'Kenneth M. Merz Jr.'] The sample-based quantum diagonalization (SQD) method shows great promise in quantum-centric simulations of ground state energies in molecular systems. Inclusion of solute-solvent interactions in…
Paul Katzberger, Sereina Riniker
Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has thereby a large impact. Implicit solvent representations are efficient but in many cases not accurate enough…
Danil Kaliakin, Akhil Shajan, Fangchun Liang, Kenneth M. Merz
The sample-based quantum diagonalization (SQD) method shows great promise in quantum-centric simulations of ground state energies in molecular systems. Inclusion of solute-solvent interactions in simulations of electronic structure is critical for biochemical and medical applications. However, all of the previous…
Jens Kleinjung, Franca Fraternali
Title: Highlights 1. • Implicit solvent replaces explicit water by a potential of mean force. 2. • Popular models are SASA, VOL and Generalized Born. 3. • Implicit solvent is used in MD, protein modelling, folding, design, prediction and drug screening. 4. • Large-scale simulations allow for parametrisation via force…
Yaoyi Chen, Andreas Krämer, Nicholas E. Charron, Brooke E. Husic + 2 more
'Cecilia Clementi' 'Frank Noé'] Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the solvent in a mean-field fashion with implicit…
Authors not listed
Understanding and manipulating the conformational behavior of a molecule in different solvent environments is of great interest in the fields of drug discovery and organic synthesis. Molecular dynamics (MD) simulations with solvent molecules explicitly present are the gold standard to compute such conformational…
Daniel J. Fowles, Benedict J. Connaughton, James W. Carter, John B. O. Mitchell + 1 more
Solubility Prediction for Organic Molecules Authors: ['Daniel J. Fowles' 'Benedict J. Connaughton' 'James W. Carter' 'John B. O. Mitchell' 'David S. Palmer'] Accurate prediction of aqueous solubility for organic molecules is of great importance across a range of fields, from the design and manufacturing of energy…
Dey, Rishabh, Michael Brocidiacono, Kushal Koirala + 2 more
The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise thermodynamic calculations. Recent advancements in machine learning (ML) present an…
Duo Song, Eric Bylaska, Maria Sushko, Kevin Rosso
Many important geochemical and biogeochemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular…
Authors not listed
Lithium-sulfur (Li/S) batteries are emerging as a next-generation energy storage technology due to their high theoretical energy density and cost-effectiveness. π-conjugated organosulfur polymers, such as poly(4-(thiophene-3-yl)benzenethiol) (PTBT), have shown promise in overcoming challenges such as the polysulfide…
Gregor N. C. Simm, Paul L. Türtscher, Markus Reiher
Solvation is a notoriously difficult and nagging problem for the rigorous theoretical description of chemistry in the liquid phase. Successes and failures of various approaches ranging from implicit solvation modeling through dielectric continuum embedding and microsolvated quantum chemical modeling to explicit…
Peter T. Lake, Max A. Mattson, Martin McCullagh
Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent implicit solvent model, IS-SPA, based on approximating the mean solvent force using the superposition approximation, provides a platform to achieve these goals. IS-SPA was originally…
Joe G Greener
Implicit solvent force fields are computationally efficient but can be unsuitable for running molecular dynamics on disordered proteins. Here I improve the a99SB-disp force field and the GBNeck2 implicit solvent model to better describe disordered proteins. Differentiable molecular simulations with 5 ns trajectories…
Joe G. Greener
Implicit solvent force fields are computationally efficient but can be unsuitable for running molecular dynamics on disordered proteins. Here I improve the a99SB-disp force field and the GBNeck2 implicit solvent model to better describe disordered proteins. Differentiable molecular simulations with 5 ns trajectories…
Authors not listed
The conformational ensemble of a molecule is strongly influenced by the surrounding environment. Correctly modeling the effect of any given environment is, hence, of pivotal importance in computational studies. Machine learning (ML) has been shown to be able to model these interactions probabilistically, with…
Kai Zhang, Zhiyu Peng, Wenfei Li, Wei Wang
Biomolecular condensates play essential roles in cellular organization and are implicated in diverse pathological processes. Their formation is driven by liquid-liquid phase separation (LLPS), a process that requires coordinated multistep desolvation of biomolecular chains and multivalent inter-chain interactions.…
Takaharu Mori, Yuji Sugita
Surfactant micelles are often utilized as membrane mimetics for structure determination and functional analysis of membrane proteins. Although curved-surface effects of the micelle can perturb their structure, it is difficult to assess such effects and membrane mimetic artifacts by experimental and theoretical methods.…
Samuel Murail, Jaysen Sawmynaden, Akli Zemirli, Maud Jusot + 4 more
Cyclic peptides are an important class of pharmaceutical drugs. We used here replica-exchange molecular dynamics (REMD) and simulated tempering (ST) simulations to explore the conformational landscape of a set of nine cyclic peptides. The N-ter to C-ter backbone cyclized peptides of seven to ten residues were…
Ziwei Chai, Sandra Luber
Based on the Solvent-Aware Interface Authors: ['Ziwei Chai' 'Sandra Luber'] In the self-consistent continuum solvation (SCCS) approach (J. Chem. Phys. 136, 064102 (2012)), the analytical expressions of the local solute-solvent interface functions determine the interface function and dielectric function values at a…
Justin Airas, Xinqiang Ding, Bin Zhang
Coarse-grained (CG) force fields are essential for molecular dynamics simulations of biomolecules, striking a balance between computational efficiency and biological realism. These simulations employ simplified models grouping atoms into interaction sites, enabling the study of complex biomolecular systems over…
Belinda Slakman, Richard West
This article reviews prior work studying reaction kinetics in solution, with the goal of using this information to improve detailed kinetic modeling in the solvent phase. Both experimental and computational methods for calculating reaction rates in liquids are reviewed. Previous studies, which used such methods to…
Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes H. Loeffler, John D. Chodera + 2 more
Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review “alchemical” approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations…