26 papers · ranked by Valyu relevance
Fabrizio Pucci, Raphaël Bourgeas, Marianne Rooman
The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to…
Stefano Zamuner, Flavio Seno, Antonio Trovato, Jerome Baudry
Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference state associated to the null interaction case. Despite their…
Stefano Zamuner, Flavio Seno, Antonio Trovato
Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference state associated to the null interaction case. Despite their…
Fabrizio Pucci, Raphael Bourgeas, Marianne Rooman
The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to…
Fabrizio Pucci, Marianne Rooman, Jacquelyn Fetrow
The unraveling and control of protein stability at different temperatures is a fundamental problem in biophysics that is substantially far from being quantitatively and accurately solved, as it requires a precise knowledge of the temperature dependence of amino acid interactions. In this paper we attempt to gain…
Martin Mechelke, Michael Habeck, Bruce R. Donald
The use of statistical potentials in NMR structure calculation improves the accuracy of the final structure but also raises issues of double counting and possible bias. Because statistical potentials are averaged over a large set of structures, they may not reflect the preferences of a particular structure or data set.…
Ya-Lan Tan, Xunxun Wang, Shixiong Yu, Bengong Zhang + 1 more
Knowledge-based statistical potentials are very important for RNA 3-dimensional (3D) structure prediction and evaluation. In recent years, various coarse-grained (CG) and all-atom models have been developed for predicting RNA 3D structures, while there is still lack of reliable CG statistical potentials not only for CG…
Sergey V. Kozyrev
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids, conformation), averaged over some balls in the spaces of sequences and…
Francesco Mancarella, Andrea Trombettoni, Giuseppe Mussardo
We determine and study the statistical interparticle potential of an ideal system of non-Abelian Chern-Simons (NACS) particles, comparing our results with the corresponding results of an ideal gas of Abelian anyons. In the Abelian case, the statistical potential depends on the statistical parameter α and it has a…
Rodrigo Cofré, Cesar Maldonado, Bruno Cessac
The Thermodynamic Formalism provides a rigorous mathematical framework for studying quantitative and qualitative aspects of dynamical systems. At its core, there is a variational principle that corresponds, in its simplest form, to the Maximum Entropy principle. It is used as a statistical inference procedure to…
J. Shepard Bryan, Prithviraj Basak, John Bechhoefer, Steve Pressé
While particle trajectories encode information on their governing potentials, potentials can be challenging to robustly extract from trajectories. Measurement errors may corrupt a particle's position, and sparse sampling of the potential limits data in higher-energy regions such as barriers. We develop a Bayesian…
J. Shepard Bryan IV, Prithviraj Basak, John Bechhoefer, Steve Pressé
Title: Summary While particle trajectories encode information on their governing potentials, potentials can be challenging to robustly extract from trajectories. Measurement errors may corrupt a particle’s position, and sparse sampling of the potential limits data in higher energy regions such as barriers. We develop a…
Christopher M. Moore, Christopher R. Stieha, Ben C. Nolting, Maria K. Cameron + 1 more
QPot (pronounced ) is an R package for analyzing two-dimensional systems of stochastic differential equations. It provides users with a wide range of tools to simulate, analyze, and visualize the dynamics of these systems. One of QPot’s key features is the computation of the quasi-potential, an important tool for…
Alejandra Durán, Sarah Marzen
Potassium voltage-gated (Kv) channels need to detect and respond to rapidly changing ionic concentrations in their environment. With an essential role in regulating electric signaling, they would be expected to be optimal sensors that evolved to predict the ionic concentrations. To explore these assumptions, we use…
Karol Capała, Bartłomiej Dybiec
Stationary states for a particle moving in a single-well, steeper than parabolic, potential driven by Lévy noise can be bi-modal. Here, we explore in details conditions that are required in order to induce multimodal stationary states having more than two modal values. Phenomenological arguments determining necessary…
Pedro B. Melo, Pedro V. Paraguassú, E. S. Nascimento, Welles A. M. Morgado
'Welles A. M. Morgado'] Brownian fluctuations arise for any quantity that depends on the stochastic variables of a Brownian particle. In this study, we explore the Brownian fluctuations of a bidimensional quadratic potential that exhibits two regimes: a confining regime and a non-confining regime. We divide the total…
Michał Cieśla, Karol Capała, Bartłomiej Dybiec
A Lévy noise is an efficient description of out-of-equilibrium systems. The presence of Lévy flights results in a plenitude of noise-induced phenomena. Among others, Lévy flights can produce stationary states with more than one modal value in single-well potentials. Here, we explore stationary states in special…
Tomáš Stejskal, Silvia Maláková, Marcela Lascsáková, Peter Frankovský + 1 more
'Peter Frankovský' 'Antonio Santagata'] Topological optimization uses two main optimization conditions aimed at achieving the maximum stiffness at minimum weight of the loaded object, while not exceeding the allowable stress. This process naturally creates complex structures with varying degrees of density. There is a…
Sara Giarrusso, Paola Gori-Giorgi, Federica Agostini
We generalize the definitions of local scalar potentials named vkin and vN−1, which are relevant to properly describe phenomena such as molecular dissociation with density-functional theory, to the case in which the electronic wavefunction corresponds to a complex current-carrying state. In such a case, an extra term…
Authors not listed
We developed OpenStats, a user-friendly web application that brings the power of the R language to researchers through a high-level interface and broad support for statistical methods such as t-tests and ANOVA. OpenStats was integrated into our electronic lab notebook Chemotion ELN via its third-party API, enabling…
Authors not listed
The rapid growth of worldwide computing power has transformed in silico chemistry into a discipline that is integrated into the daily work of many chemists. Nowadays, researchers find it increasingly straightforward to predict a wide range of molecular properties and chemi- cal processes at reasonable computational…
Pierre Le Doussal, Grégory Schehr
one-dimensional trapped Riesz gas Authors: ['Pierre Le Doussal' 'Grégory Schehr'] We consider the classical trapped Riesz gas, i.e., N particles at positions xi in one dimension with a repulsive power law interacting potential ∝ 1/|xi − xj | k , with k > −2, in an external confining potential of the form V (x) ∼ |x| n…
M. Kurzynski, P. Chelminiak
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics of conformational transitions which often manifests in fluctuating rates of the catalyzed processes…
Charles Sing, Jian Qin
Complex coacervation is a phase separation phenomenon, driven by the electrostatic attraction between oppositely-charged macromolecular species. A recent surge of interest in coacervation between polyelectrolytes has been driven by both fundamental advances in experimental characterization of these systems, along with…
Brittany Story, Biswajit Sadhu, Henry Adams, Aurora Clark
Recent work (J. Chem. Phys. 154, 114114) has demonstrated that sublevelset persistent homology provides a compact representation of the complex features of an energy landscape in $3N$-dimensions. This includes information about all transition paths between local minima (connected by critical points of index > 1), and…
Authors not listed
This paper introduces simple phenomenological rate theory from the perspective of molecular interconversions and then applies it, in the form of Transition State Theory, to processes such as atomic diffusion and thermally-activated crystal growth in condensed matter composed of very large numbers of atoms or molecules.…