24 papers · ranked by Valyu relevance
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…
James P. Roney, Chenxi Ou, Sergey Ovchinnikov
Machine learning has driven rapid progress in protein structure prediction and design, but key challenges remain such as predicting protein structures when evolutionary information is unavailable, modeling full conformational landscapes, and capturing the thermodynamics of mutations and conformational changes. To…
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…
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…
Adrien Vacher, François-Xavier Vialard
In this note, we derive upper-bounds on the statistical estimation rates of unbalanced optimal transport (UOT) maps for the quadratic cost. Our work relies on the stability of the semi-dual formulation of optimal transport (OT) extended to the unbalanced case. Depending on the considered variant of UOT, our stability…
Amir Hossein Khorram manesh, J. Sadeghi, Saeed Noori Gashti
statistical and superstatistical perspectives with various distributions Authors: ['Amir Hossein Khorram manesh' 'J. Sadeghi' 'Saeed Noori Gashti'] The Hulth´en potential is a short-range potential that has been widely used in various fields of physics. In this paper, we investigate the distribution functions for the…
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…
Theo Desachy, Marc Thevenet, Samuel Garcia, Anistasha Lightning + 3 more
Studies with low statistical power reduce the probability of detecting true effects and often lead to overestimated effect sizes, undermining the reproducibility of scientific results. While several free statistical software tools are available for calculating statistical power, they often do not account for the…
M. Vlad, D. I. Palade, F. Spineanu
Turbulence is a complex nonlinear process, which appears in many domains as fluid mechanics, plasma physics, astrophysics, atmosphere and ocean sciences, chemistry [1]-[3]. One of the main difficulty in understanding the dynamics of turbulence is the complicated combination of stochastic and quasi-coherent aspects that…
Michał Mandrysz, Bartłomiej Dybiec, Gianpiero Colonna
The properties of dynamical systems driven by noise are determined by the combined action of deterministic forces and random fluctuations. The action of non-white (correlated) noise is capable of producing stationary states with a number of modes larger than the number of (stable) fixed points of the deterministic…
Radu V. Craiu, Ruobin Gong, Xiao-Li Meng
This article proposes a set of categories, each one representing a particular distillation of important statistical ideas. Each category is labeled a "sense" because we think of these as essential in helping every statistical mind connect in constructive and insightful ways with statistical theory, methodologies, and…
Reza Hosseini, Samin Tajik, Zahra Koohi Lai, Tayeb Jamali + 3 more
'Emmanuel Haven' 'Reza Jafari' 'Rosario Lo Franco'] We have implemented quantum modeling mainly based on Bohmian mechanics to study time series that contain strong coupling between their events. Compared to time series with normal densities, such time series are associated with rare events. Hence, employing Gaussian…
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…
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…
Ammon E. Posey, Anne Bremer, Nadia A. Erkamp, Avnika Pant + 4 more
Biomolecular condensates form via processes that combine phase separation and reversible associations of multivalent macromolecules. Condensates can be two- or multi-phase systems defined by coexisting dense and dilute phases. Here, we show that solution ions can partition asymmetrically across coexisting phases…
Sara C. Quintanilha Valente, Rodrigo da Costa Lima Bruni, Zochil González Arenas, Daniel G. Barci + 2 more
'Zochil González Arenas' 'Daniel G. Barci' 'José María Amigó' 'Fernando Montani'] This study explores the escape dynamics of bistable systems influenced by multiplicative noise, extending the classical Kramers rate formula to scenarios involving state-dependent diffusion in asymmetric potentials. Using a generalized…
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…
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…
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…
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…
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.…
Pilhwa Lee
Electrodiffusion is essential in understanding the mechanisms of electrophysiology. Active exchange pumps are critical regarding volume homeostasis, and are also significant in the mechanisms of cell division, growth, and apoptosis. In the formalism of the immersed boundary (IB) method, we replace classical interface…