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…
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…
Xin Cao, Michelle Hummel, Yuzhang Wang, Carlos Simmerling + 1 more
'Evangelos A. Coutsias'] In this paper, we present dSASA (differentiable SASA), an exact geometric method to calculate solvent accessible surface area (SASA) analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to tetrahedra in groups of four atoms by Delaunay tetrahedrization…
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…
In Jung Kim, Hyuntae Na, Ozlem Keskin
The solvent accessible surface area and the solvent accessible volume are measurements commonly used in implicit solvent models to include the effect of forces exerted by solvents on the protein surfaces (or the atoms on protein surfaces). The two measurements have limitations in describing interactions between…
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…
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…
Clare Xie Yijia, Julian Becker, Tom Welton, Patricia A. Hunt
The interactions of ionic liquids (ILs) with organic solutes are of interest to many applications involving the use of ILs as task-specific solvents, such as in sensing devices or catalysis. However, currently little is known about these specific interactions. The interactions of two structurally-similar organic…
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.…
Yanfei Tang, John E. McLaughlan, Gary S. Grest, Shengfeng Cheng + 1 more
'Aleksandar Y. Mehandzhiyski'] A method of simulating the drying process of a soft matter solution with an implicit solvent model by moving the liquid-vapor interface is applied to various solution films and droplets. For a solution of a polymer and nanoparticles, we observe “polymer-on-top” stratification, similar to…
Hao Xiao
environments via cylindrical coordinates Authors: ['Hao Xiao'] Abstract. This paper characterizes sharp solute-solvent interfaces in hydrophobic environments, and there are three major ingredients. The first is the variational implicit solvent model (VISM) which establishes the free energy functional of arbitrary…
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…
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…
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…
Jeffry Setiadi, Simon Boothroyd, David Slochower, David Dotson + 4 more
Software to more rapidly and accurately predict protein--ligand binding affinities is of high interest for early-stage drug discovery, and physics-based methods are among the most widely used technologies for this purpose. The accuracy of these methods depends critically on the accuracy of the potential functions they…
Julie A. Harris, Ruibin Liu, Vinicius Martins de Oliveira, Erik Vaquez Montelongo + 2 more
Constant pH molecular dynamics (MD) simulations sample protonation states on the fly according to the conformational environment and user specified pH condition; however, the accuracy of most current applications is limited due to the use of implicit-solvent models or hybrid solvent scheme. Here we report the first…