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The biophysical analysis of dynamically formed multi-protein complexes in solution presents a formidable technical challenge. Sedimentation velocity (SV) analytical ultracentrifugation achieves strongly size-dependent hydrodynamic…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical…
With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
A first-principles study of the adsorption of a single water molecule on a layer of graphitic carbon nitride employing an embedding approach is presented. The embedding approach involves an algorithm to obtain localized Wannier orbitals of…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account.…
Electrochemical devices often consist of multicomponent electrolyte solutions. Two processes influence the overall dynamics of these devices: the formation of electrical double layers and chemical conversion due to redox reactions. However,…
A novel global energy model for multi-class semantic image segmentation is proposed that admits very efficient exact inference and derivative calculations for learning. Inference in this model is equivalent to MAP inference in a particular…
We present the theory, implementation, and benchmarking of a real-time time-dependent density functional theory (RT-TDDFT) module within the RMG code, designed to simulate the electronic response of molecular systems to external…
The matrix element method utilizes ab initio calculations of probability densities as powerful discriminants for processes of interest in experimental particle physics. The method has already been used successfully at previous and current…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
Many objects of nanoscopic dimensions involve fluid-tethered chain interfaces. These systems are of interest for basic science and for several applications, in particular for design of nanodevices for specific purposes. We review recent…
The use of machine learning algorithms to predict behaviors of complex systems is booming. However, the key to an effective use of machine learning tools in multi-physics problems, including combustion, is to couple them to physical and…
It has become increasingly clear that a full understanding of the physics of electrons in disordered systems requires an approach in which both disorder and interactions are taken into account. Work on small numbers of electrons has…
In this work, we investigate dispersion interactions in a selection of atomic, molecular, and molecule-surface systems, comparing high-level correlated methods with empirically-corrected density functional theory (DFT). We assess the…
We study dynamics of clustering in systems containing active particles that are immersed in an explicit solvent. For this purpose we have adopted a hybrid simulation method, consisting of molecular dynamics and multi-particle collision…
Granular intrusion is commonly observed in natural and human-made settings. Unlike typical solids and fluids, granular media can simultaneously display fluid-like and solid-like characteristics in a variety of intrusion scenarios. This…
Smoothed dissipative particle dynamics (SDPD) is a widely used particle-based method for modelling soft matter systems at mesoscopic and macroscopic scales, offering thermodynamic consistency and direct control over the fluid's transport…
Electronic polarization and dispersion are decisive actors in determining interaction energies between molecules. These interactions have a particularly profound effect on excitation energies of molecules in complex environments, especially…
In this paper we study the practicality and usefulness of incorporating distributed representations of graphs into models within the context of drug pair scoring. We argue that the real world growth and update cycles of drug pair scoring…