Related papers: Atomic Biology, Electrostatics, and Ionic Channels
Radioactive molecules provide a powerful new platform in the search for new physics at energy scales complementary to high-energy particle colliders. By combining enhancements from nuclear properties with the sensitivity and control offered…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various…
The intrinsic dynamics of a system with open decay channels is described by an effective non-Hermitian Hamiltonian which at the same time allows one to find the external dynamics, - reaction cross sections. We discuss ways of incorporating…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
Electrochemical phenomena in biology often unfold in confined geometries where micrometer- to millimeter-scale domains coexist with nanometer-scale interfacial diffuse charge layers. We analyze a model lipid membrane-electrolyte system…
Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play…
Mixtures of active and passive particles are ubiquitous at the microscale. Many essential microbial processes involve interactions with dead or immotile cells or passive crowders. When passive objects are immersed in active baths, their…
In conventional optical Stark-shift spectroscopy, molecules are exposed to spatially homogeneous static electric fields that shift the energies of their spectral lines. These shifts are attributed to the molecular electronic properties,…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
We have developed a molecular mean-field theory -- fourth-order Poisson-Nernst-Planck-Bikerman theory -- for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with…
Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental…
The paper shows how the diffusive movement of ions through a channel protein can be described as a chemical reaction over an arbitrary shaped potential barrier. The result is simple and intuitive but without approximation beyond the…
The application of molecular dynamics (MD) simulations to the interpretation of Raman scattering spectra is hindered by inability of atomistic simulations to account for the dynamic evolution of electronic polarizability, requiring the use…
Hydrogen-bond networks govern molecular structure and function across chemistry, biology and materials science, yet their deterministic control at the atomic scale remains a central challenge (1-9).Here, we directly visualize how an…
Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate…
Potassium (K-) channels catalyze K+ ion permeation across cellular membranes while simultaneously discriminating their permeation over Na+ ions by more than a factor of a thousand. Structural studies show bare K+ ions occupying the…
The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…