24 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…
José A. Villegas, Emmanuel D. Levy
Membraneless organelles are cellular compartments that form by liquid-liquid phase separation of one or more components. Other molecules, such as other proteins and nucleic acids, will distribute between the cytoplasm and the liquid compartment in accordance with the thermodynamic drive to lower the free energy of the…
Dezső Boda
The particles of electrorheological fluids can be modelled as dielectric spheres (DS) immersed in a continuum dielectric. When an external field is applied, polarization charges are induced on the surfaces of the spheres and can be represented as point dipoles placed in the centres of the spheres. When the DSs are…
Robin Guttmann, Johannes Hoja, Christoph Lechner, Reinhard J Maurer + 2 more
'Alexander F Sax' 'Peter Schreiner'] Weak molecular interactions (WMI) are responsible for processes such as physisorption; they are essential for the structure and stability of interfaces, and for bulk properties of liquids and molecular crystals. The dispersion interaction is one of the four basic interactions types…
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…
C. D. Fosco, Fernando C. Lombardo, Francisco D. Mazzitelli
We evaluate the electrostatic interaction energy between two surfaces, one flat and the other slightly curved, in terms of the two-point autocorrelation functions for patch potentials on each one of them, and of a single function ψ which defines the curved surface. The resulting interaction energy, a functional of ψ…
Cristian Zagar, Ryan-Rys Griffith, Rudolf Podgornik, Alexei A. Kornyshev
'Alexei A. Kornyshev'] Research in the field of nanoplasmonic metamaterials is moving towards more and more interesting and, potentially useful, applications. The present work tackles the problem of nanoparticle self-assembly at an electrochemical solid-liquid interface from a purely theoretical perspective. We perform…
István P. Sugár, Francisco Monroy
By using the recently generalized version of Newton’s shell theorem, analytical equations are derived to calculate the electric interaction energy between two separated, charged spheres surrounded outside and inside by electrolyte. This electric interaction energy is calculated as a function of the electrolyte’s ion…
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…
O. I. Obolensky, T. P. Doerr, Yi-Kuo Yu
Electrostatic interactions among colloidal particles are often described using the venerable (two-particle) Derjaguin-Landau-Verwey-Overbeek (DLVO) approximation and its various modifications. However, until the recent development of a many-body theory exact at the Debye-Hückel level (Yu in Phys Rev E 102:052404…
Muhammad Hassan, Connor Williamson, Joshua Baptiste, Stefanie Braun + 3 more
between Dielectric Particles with Electric Fields: A General Electrostatic Many-Body Framework Authors: ['Muhammad Hassan' 'Connor Williamson' 'Joshua Baptiste' 'Stefanie Braun' 'Anthony J. Stace' 'Elena Besley' 'Benjamin Stamm'] We derive a rigorous analytical formalism and propose a numerical method for the…
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…
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…
Alžbeta Kubincová, Philippe H. Hünenberger, Madhavi Krishnan
Over the past few decades the experimental literature has consistently reported observations of attraction between like-charged colloidal particles and macromolecules in solution. Examples include nucleic acids and colloidal particles in bulk solution and under confinement, and biological liquid-liquid phase…
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…
Alexander Kolpakov, A. G. Kolpakov
Since the Schr¨odinger equation for particle systems is invariant with respect to translations and rotations [1], every "rigid" quantum system can move as a "rigid body" without any change of its relative characteristics, in particular, without any change of its total energy. However, the total energy of several…
Andrii Kleshchonok, Alexandre Tkatchenko
van der Waals (vdW) dispersion interactions strongly impact the properties of molecules and materials. Often, the description of vdW interactions should account for the coupling with pervasive electric fields, stemming from membranes, ionic channels, liquids, or nearby charged functional groups. However, this…
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…
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…
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…
Raghavender Surya Upadhyayula
Protein complexes with short linear motifs (SLiMs) are known to play important regulatory functions in eukaryotes. In this investigation, I have studied the structures deposited in PDB with SLiMs. The structures Were grouped into three broad categories of protein-protein, protein-peptide and the rest as others.…
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…
Taylor Schaffner, Benjamin Machta
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we present a model and a Monte Carlo simulation framework to investigate how changes…