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Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…

Chemical Physics · Physics 2025-10-10 Juan Viguera Diez , Mathias Schreiner , Simon Olsson

Two types of approaches to modeling molecular systems have demonstrated high practical efficiency. Density functional theory (DFT), the most widely used quantum chemical method, is a physical approach predicting energies and electron…

Chemical Physics · Physics 2020-03-02 Anton V. Sinitskiy , Vijay S. Pande

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the…

Quantitative Methods · Quantitative Biology 2023-08-24 Enze Ye , Yuhang Wang , Hong Zhang , Yiqin Gao , Huan Wang , He Sun

We develop a new quantitative molecular theory of liquid-phase dipolar polymer gels. We model monomer units of the polymer network as a couple of charged sites separated by a fluctuating distance. For the first time, within the random phase…

Soft Condensed Matter · Physics 2021-03-09 Yury A. Budkov , Nikolai N. Kalikin , Andrei L. Kolesnikov

We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic…

Biomolecules · Quantitative Biology 2011-08-01 Fabio Pichierri

Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…

Atomic Physics · Physics 2013-05-14 Stefan Pabst

Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…

Chemical Physics · Physics 2015-06-12 Michele Pavanello , Troy Van Voorhis , Lucas Visscher , Johannes Neugebauer

We present a self-consistent kinetic theory for the electronic response of a plasma-facing dielectric solid. Based on the Poisson equation and two sets of spatially separated Boltzmann equations, one for electrons and ions in the plasma and…

Plasma Physics · Physics 2017-08-02 Franz X. Bronold , Holger Fehske

We construct a tensor model for nematic phases of bent-core molecules from molecular theory. The form of free energy is determined by molecular symmetry, which includes the couplings and derivatives of a vector and two second-order tensors,…

Soft Condensed Matter · Physics 2018-08-24 Jie Xu , Fangfu Ye , Pingwen Zhang

Following two recent papers [Phys. Chem. Chem. Phys. 2015, \textbf{17}, 3196; Mol. Phys. 2015, \textbf{113}, 1843], we perform a larger-scale study of chemical structure in one dimension (1D). We identify a wide, and occasionally…

Chemical Physics · Physics 2017-05-01 Caleb J. Ball , Pierre-François Loos , P. M. W. Gill

The behavior of a strongly charged polymer adsorbed on an oppositely charged surface of low-dielectric constant is formulated by the functional integral method. By separating the translational, conformational, and fluctuational degrees of…

Soft Condensed Matter · Physics 2007-05-23 Chi-Ho Cheng , Pik-Yin Lai

We consider molecular communication networks consisting of transmitters and receivers distributed in a fluidic medium. In such networks, a transmitter sends one or more signalling molecules, which are diffused over the medium, to the…

Computational Engineering, Finance, and Science · Computer Science 2015-03-20 Chun Tung Chou

Understanding the electronic and phononic transport properties of junctions consisting of a scattering region such as a nanoscale matters or molecules connected to two or more electrodes is the central basis for future nano and molecular…

Mesoscale and Nanoscale Physics · Physics 2016-07-11 Hatef Sadeghi

A simple and efficient analytical model is proposed for analyzing plasmonic phenomena arising in nanoscale defects on metal surfaces, specifically low aspect ratio dome-shaped protrusions and depressions. The model enables the calculation,…

Optics · Physics 2025-07-03 Anton V. Dyshlyuk , Oleg B. Vitrik

High-entropy pyrochlore oxides possess ultra-low thermal conductivity and excellent high-temperature phase stability, making them promising candidate for next-generation thermal barrier coating (TBC) materials. However, reliable predictive…

Materials Science · Physics 2025-07-24 Yuxuan Wang , Guoqiang Lan , Huicong Chen , Jun Song

We present a unifying framework that allows us to study the mixed crystalline-electromagnetic responses of topological semimetals in spatial dimensions up to $D = 3$ through dimensional augmentation and reduction procedures. We show how…

Mesoscale and Nanoscale Physics · Physics 2023-09-21 Mark R. Hirsbrunner , Oleg Dubinkin , Fiona J. Burnell , Taylor L. Hughes

Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…

Statistical Mechanics · Physics 2009-02-12 Michael Bachmann , Wolfhard Janke

We present a theory of the dielectric response of a solution containing large solutes, of a nanometer size, in a molecular solvent. It combines the molecular dipole moment of the solute with the polarization of a large subensemble of…

Biological Physics · Physics 2015-06-04 Dmitry V. Matyushov

The limited extrapolative power of structure-based machine learning (ML) models is a critical bottleneck in chemical discovery, particularly for industrial R&D, where navigating uncharted chemical space to find next-generation materials or…

The electrostatic potential in the neighborhood of a biomolecule can be computed thanks to the non-linear divergence-form elliptic Poisson-Boltzmann PDE. Dedicated Monte-Carlo methods have been developed to solve its linearized version (see…

Numerical Analysis · Mathematics 2016-11-15 Mireille Bossy , Nicolas Champagnat , Helene Leman , Sylvain Maire , Laurent Violeau , Mariette Yvinec