25 papers · ranked by Valyu relevance
Ella M. King, Megan C. Engel, Caroline Martin, Alp M. Sunol + 4 more
'Qian-Ze Zhu' 'Sam Schoenholz' 'Vinothan Manoharan' 'Michael P. Brenner'] Accurate interaction potentials between microscopic components such as colloidal particles or cells are crucial to understanding a range of processes, including colloidal crystallization, bacterial colony formation, and cancer metastasis. Even in…
Junwen Wang, Shengfeng Cheng
A compact analytical form is derived through an integration approach for the interaction between a sphere and a thin rod of finite and infinite lengths, with each object treated as a continuous medium of material points interacting by the Lennard-Jones 12-6 potential and the total interaction potential as a summation…
Anna Luisa Upterworth, Daniel Sebastiani
Strength in Simulations of Liquid Mixtures: A Configuration-Dependent Species-Specific Measure of Interaction Enthalpies Authors: ['Anna Luisa Upterworth' 'Daniel Sebastiani'] The thermodynamics of mixing and demixing of molecular liquids poses a perpetual challenge for atomistic simulations. We provide a computational…
Sida Wang, Rowan Walker-Gibbons, Bethany Watkins, Melissa Flynn + 1 more
'Madhavi Krishnan'] The interaction between charged objects in solution is generally expected to recapitulate two central principles of electromagnetics: (1) like-charged objects repel, and (2) they do so regardless of the sign of their electrical charge. Here we demonstrate experimentally that the solvent plays a…
J. C. Fernandes, J. P. Ferreira, F. E. Barone, F. A. Barone + 2 more
In this paper, we explore the Klein–Gordon field theory in (D + 1) dimensions in the presence of a (D − 1)-dimensional hyperplanar δ-like potential that couples quadratically to the field derivatives. This model effectively generalizes the Neumann boundary condition for the scalar field on the plane, as it reduces to…
John Herbert, Suranjan Paul
Soft anions exhibit surface activity at the air/water interface that can be probed using surface-sensitive vibrational spectroscopy, yet the statistical mechanics behind this surface activity remains a matter of debate. Here, we examine the nature of anion--water interactions at the air/water interface using a…
L. H. C. Borges, C. Filgueiras, F. A. Barone, A. A. Nogueira
In this paper, we investigate novel classical non-local effects in scalar field theory arising from the presence of external sources and a material boundary. Specifically, we consider a model in which the standard Klein-Gordon field theory is modified by a non-local term. First, we analyze the interaction between…
Jane S. Murray, Ángel Martín Pendás
This paper discusses two quite different computational experiments relating to the formation of σ-hole bonds A···B. The first involves looking at the complex at equilibrium and finding the contour X of the electronic density which allows the iso-density envelopes of A and B to be nearly touching. This contour…
Johannes Henrichsmeyer, Michael Thelen, Reinhold F. Fink
It is shown that the exchange repulsion energy, Exr, can be rationalized by partitioning the respective energy expression for two systems with Hartree-Fock orbitals into physically meaningful contributions. A division of Exr into a positive kinetic and a negative potential part is possible, but these contributions…
Farideh Badichi Akher, Yinan Shu, Zoltan Varga, Suman Bhaumik + 1 more
Machine-learned representations of potential energy surfaces generated in the output layer of a feedforward neural network are becoming increasingly popular. One difficulty with neural-network output is that it is often unreliable in regions where training data is missing or sparse. Humandesigned potentials often build…
Julia Nauman, Dylan Suvlu, Adam Willard
In this manuscript, we explore the electrostatic environment of the interface between a solid and a dilute electrolyte solution, with an emphasis on the electric field profiles that these systems produce. We review the theoretical formalism that connects electrostatic potential profiles, electric field profiles, and…
Josef Paul Kynast, Felix Schwägerl, Birte Höcker
Recognition of specific molecules by proteins is a fundamental cellular mechanism and relevant for many applications. Being able to modify binding is a key interest and can be achieved by repurposing established interaction motifs. We were specifically interested in a methodology for the design of peptide binding…
Charles T. Sebens
In electrostatics, we can use either potential energy or field energy to ensure conservation of energy. In electrodynamics, the former option is unavailable. To ensure conservation of energy, we must attribute energy to the electromagnetic field and, in particular, to electromagnetic radiation. If we adopt the standard…
Anthony Gurunian, Keren Lasker, Ashok A. Deniz
Biomolecular condensates are a ubiquitous component of cells, known for their ability to selectively partition and compartmentalize biomolecules without the need for a lipid membrane. Nevertheless, condensates have been shown to interact with lipid membranes in diverse biological processes, such as autophagy and T-cell…
Authors not listed
Periodic boundary condition-adapted formulations of quantum mechanics/molecular mechanics (QM/MM) methods enable the extraction of accurate free energies, provided that efficient phase-space sampling is achieved. In this work, we develop a thermodynamic integration scheme based on an electrostatic embedding QM/MM…
Mohammad Reza Karimpour, Dmitry V. Fedorov, Alexandre Tkatchenko
We employ various quantum-mechanical approaches for studying the impact of electric fields on both nonretarded and retarded noncovalent interactions between atoms or molecules. To this end, we apply perturbative and non-perturbative methods within the frameworks of quantum mechanics as well as quantum electrodynamics.…
Mohammad Reza Karimpour, Dmitry V. Fedorov, Alexandre Tkatchenko
By means of quantum mechanics and quantum electrodynamics applied to coupled harmonic Drude oscillators, we study the interaction between two neutral atoms or molecules subject to a uniform static electric field. Our focus is to understand the interplay between leading contributions to field-induced…
Sonata Kvedaravičiūtė, David Carrasco-Busturia, Klaus B. Møller, Jógvan Magnus Haugaard Olsen
We present a fully self-consistent polarizable embedding (PE) model that does not suffer from unphysical boundary polarization. This is achieved through the use of the minimum-image convention (MIC) in the induced electrostatics. It is a simple yet effective approach that includes a more physically accurate description…
Ernesto Fajardo-Díaz, Emmanuelle Bignon, François Dehez, Yasaman Karami + 1 more
Molecular dynamics is a key technique for exploring biomolecular systems at the atomic level. The rapid growth in accessible system sizes and timescales has intensified the need for efficient post-processing methods that extract meaningful insights from the resulting data. Interaction fingerprint (IFP) analyses are a…
L. Saba, C. D. Fosco
The van der Waals interaction between neutral atoms is typically studied using stationary perturbation theory for the short-distance (London) limit, while longdistance (Casimir-Polder) results are usually derived via semiclassical, time-dependent approaches. In this pedagogical article, we demonstrate that…
Tom Miclot, Stepan Timr
Protein-protein interactions (PPIs) are fundamental to virtually all cellular processes; however, elucidating the principles that govern protein association into complexes remains a significant challenge. In this study, we present a comparative analysis of stable and transient protein interfaces, offering a detailed…
Marvin Scherlo, Elias Wippermann, Torben Fürtges, Ricarda Künne + 5 more
Molecular interactions govern cellular function, making them essential to discover biomolecular mechanisms by unravelling structure-function relationships. The rapid growth of AI-based prediction, experimental determination, and molecular dynamics simulations generates structural data at an unprecedented scale.…
Fodil Azzaz, Jacques Fantini
Understanding molecular interactions at the atomic level remains a central challenge across biology, medicine, and engineering. We introduce Perturbation Scanning (PS), an interrogative AI framework that actively deconstructs molecular interfaces. PS integrates graph-based representations of structures derived from…
Hossein Moghimianavval, Chintan Patel, Sonisilpa Mohapatra, Sung-Won Hwang + 4 more
Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane…
Marko Melander, Tongwei Wu, Karoliina Honkala
Electrochemical interfaces and reactions play a decisive role in \textit{e.g.} clean energy conversion but understanding their complex chemistry remains an outstanding challenge. Constant potential or grand canonical ensemble (GCE) simulations are indispensable for unraveling the properties of electrochemical processes…