Related papers: Atomic Biology, Electrostatics, and Ionic Channels
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
Electrostatic correlations play an important role in physics, chemistry and biology. In plasmas they lead to thermodynamic instability similar to the liquid-gas phase transition of simple molecular fluids. For charged colloidal suspensions…
Angstrom-scale fluidic channels are ubiquitous in nature, and play an important role in regulating cellular traffic, signaling, and responding to stimuli. Synthetic channels are now a reality with the emergence of several cutting-edge…
This review presents some of the challenges in constructing models of atomic nuclei starting from theoretical descriptions of the strong interaction between nucleons. The focus is on statistical computing and methods for analyzing the link…
Biological macromolecules including nucleic acids, proteins, and glycosaminoglycans are typically anionic and can span domains of up to hundreds of nanometers and even micron length scales. The structures exist in crowded environments that…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Correspondences between the Thomson Problem and atomic electron shell-filling patterns are observed as systematic non-uniformities in the distribution of potential energy necessary to change configurations of $N\le 100$ electrons into…
Diffusion models are important in tissue engineering as they enable an understanding of molecular delivery to cells in tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically…
Natural evolution gives the impression of leading to an open-ended process of increasing diversity and complexity. If our goal is to produce such open-endedness artificially, this suggests an approach driven by evolutionary metaphor. On the…
Quasi-static models of barrier suppression have played a major role in our understanding of the ionization of atoms and molecules in strong laser fields. Despite their success, in the case of diatomic molecules these studies have so far…
An overview of recent data on electromagnetic hadron form factors is presented and discussed in terms of selected nucleon models in space-like and time-like regions. Model independent properties connecting scattering and annihilation…
Artificial and natural neural network models are a new toolkit which could be potentially have been used for clarifying of complex brain functions. To attend this goal, such models need to be neurobiologically realistic. However, although…
A wide variety of biological as well as non-biological processes and phenomena involving ion channels, binding, pH, folding/unfolding and effects of chain length are well represented by multiphasic profiles, a series of straight lines…
The transport and dispersion of multiple species of charged ions are central to many biological and physical processes, including electrokinetic ion separation. However, most theoretical studies of dispersion in channels have focused on…
In this article we address the three-dimensional modeling and simulation of biological ion channels using a continuum-based approach. Our multi-physics formulation self-consistently combines, to the best of our knowledge for the first time,…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
We provide a brief review of the common assumptions about biological learning with findings from experimental neuroscience and contrast them with the efficiency of gradient-based learning in recurrent neural networks. The key issues…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Atomic nuclei are complex, quantum many-body systems whose structure manifests itself through intrinsic quantum states associated with different excitation modes or degrees of freedom. Collective modes (vibration and/or rotation) dominate…