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Quantum mechanics/molecular mechanics (QM/MM) is a standard computational tool for describing chemical reactivity in systems with many degrees of freedom, including polymers, enzymes, and reacting molecules in complex solvents. However,…

Chemical Physics · Physics 2020-07-22 Alexander V. Mironenko , Gregory A. Voth

This work represents an extension of mesoscale particle-based modeling of electrophoretic deposition (EPD), which has relied exclusively on pairwise interparticle interactions described by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory.…

Piezoelectrics have long been studied using parameterized models fit to experimental data, starting with the work of Devonshire in 1954. Much has been learned using such approaches, but they can also miss major phenomena if the materials…

Materials Science · Physics 2020-03-05 R. E. Cohen

The lack of inversion symmetry in semiconducting transition metal dichalcogenide monolayers (TMDMs) enables a considerable molecular-level intrinsic piezoelectricity, which opens prospects for atomically-thin piezotronics and…

Mesoscale and Nanoscale Physics · Physics 2018-09-12 Yunhua Wang , Zongtan Wang , Jie Li , Jie Tan , Biao Wang , Yulan Liu

Molecular communications (MC), where molecules are used to encode, transmit, and receive information, is a promising means of enabling the coordination of nanoscale devices. The paradigm has been extensively studied from various aspects,…

Emerging Technologies · Computer Science 2016-03-29 Murat Kuscu , Ozgur B. Akan

Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…

Soft Condensed Matter · Physics 2020-11-13 K. Koperwas , A. Grzybowski , M. Paluch

We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…

Computational Physics · Physics 2017-04-05 Gregor Mitscha-Baude , Andreas Buttinger-Kreuzhuber , Gerhard Tulzer , Clemens Heitzinger

While the properties of materials at microscopic scales are well described by fundamental quantum mechanical equations and electronic structure theories, the emergent behavior of mesoscopic or macroscopic composites is no longer governed…

Applied Physics · Physics 2025-07-10 Lifeng Hao , Fan Li , Yongqi Li , Siyong Wang , Xiaodong He

Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…

Numerical Analysis · Mathematics 2015-06-09 Gideon Simpson , Mitchell Luskin , David J. Srolovitz

Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have employed strings, fingerprints, global…

Machine Learning · Computer Science 2025-05-28 Daniil A. Boiko , Thiago Reschützegger , Benjamin Sanchez-Lengeling , Samuel M. Blau , Gabe Gomes

Rapid emergence of the multimodal imaging in scanning probe, electron, and optical microscopies have brought forth the challenge of understanding the information contained in these complex data sets, targeting both the intrinsic…

Materials Science · Physics 2021-10-14 Yongtao Liu , Maxim Ziatdinov , Sergei V. Kalinin

In the development of active animate materials, electromechanical coupling is highly attractive to realize mechanoresponsive functionality. Piezoelectricity is the most utilized electromechanical phenomenon due to the wide availability of…

In this paper, we introduce a new scheme for the efficient numerical treatment of the electronic Schr\"odinger equation for molecules. It is based on the combination of a many-body expansion, which corresponds to the so-called bond order…

Numerical Analysis · Mathematics 2017-07-20 Sambasiva Rao Chinnamsetty , Michael Griebel , Jan Hamaekers

In this paper, we present an analytical model for a diffusive molecular communication (MC) system with a reversible adsorption receiver in a fluid environment. The time-varying spatial distribution of the information molecules under the…

Information Theory · Computer Science 2016-04-08 Yansha Deng , Adam Noel , Maged Elkashlan , Arumugam Nallanathan , Karen C. Cheung

After two decades of a development of the unitary and analytic models of the electromagnetic structure of hadrons and nuclei their main principles are briefly formulated, then a general scheme of their applications to the electromagnetic,…

High Energy Physics - Phenomenology · Physics 2007-05-23 S. Dubnicka , A. Z. Dubnickova , P. Strizenec

After a brief introduction to the field of light-responsive materials, this paper provides a general theory for modeling the photomechanical response of a material, applies it to the two best-known mechanisms of photothermal heating and…

Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In…

Soft Condensed Matter · Physics 2009-11-11 E. Salonen , E. Terama , I. Vattulainen , M. Karttunen

We introduce a mathematical framework for retrosynthetic analysis, an important research method in synthetic chemistry. Our approach represents molecules and their interaction using string diagrams in layered props - a recently introduced…

Logic in Computer Science · Computer Science 2023-11-08 Ella Gale , Leo Lobski , Fabio Zanasi

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations:…

Machine Learning · Computer Science 2025-03-12 Taojie Kuang , Qianli Ma , Athanasios V. Vasilakos , Yu Wang , Qiang , Cheng , Zhixiang Ren

Piezoelectricity, the generation of electric charge in response to mechanical stress, is a key property in both natural and synthetic materials. This study significantly boosts the piezoelectric response of chitosan, a biodegradable…