Related papers: Can we make biochemistry an exact science?
The exact renormalization group is applied to the world sheet theory describing bosonic open string backgrounds to obtain the equations of motion for the fields of the open string. Using loop variable techniques the equations can be…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
An open quantum system refers to a system that is further coupled to a bath system consisting of surrounding radiation fields, atoms, molecules, or proteins. The bath system is typically modeled by an infinite number of harmonic…
Contrary to a wide-spread commonplace, an exact, ray-based treatment holding for any kind of monochromatic wave-like features (such as diffraction and interference) is provided by the structure itself of the Helmholtz equation. This…
We show that the definition of an energy current for non-relativistic systems with action-at-a-distance is possible if the interaction respects Gausses law, i.e. if it is Coulomb-like. The energy current can transport kinetic and mass…
Most people agree that human activities are consistent with physical laws. One may naturally think that sensible economic theories can be derived from physical laws and evolutionary principles. This is indeed the case. In this paper, we…
The action principle is frequently used to derive the classical equations of motion. The action may also be used to associate group elements with curves in the space-time manifold, similar to the gauge transformations. The action principle…
In this short note we review deterministic simulation of biochemical pathways, i.e. networks of biochemical reactions obeying the law of mass action. It is meant as a basis for the MATLAB code, written by the author, which permits easy…
Since Galileo and (more recently) D'Arcy Thompson, it has been understood that physical processes and constraints influence biological structures and their resulting functions. However these cross-discpline connections -- and their…
Charge regulation is a fundamental mechanism in most chemical, geochemical, and biochemical systems. Various minerals surfaces and proteins are well-known to change their charge state as a function of the activity of the hydronium ions,…
Even after over 150 years of discussion, the interpretation of the second law of thermodynamics continues to be a source of confusion and controversy in physics. This confusion has been accentuated by recent challenges to the second law and…
The quantum dynamics of electron-nuclear systems is analyzed from the perspective of the exact factorization of the wavefunction, with the aim of defining gauge invariant equations of motion for both the nuclei and the electrons. For pure…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We consider a bound system of charged particles moving in an external electromagnetic field, including leading relativistic corrections. The difference from the point particle with a magnetic moment comes from the presence of…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a…
We have reviewed the Comment of Geyer et al. [arXiv:0708.1548] concerning our recent work [Phys. Rev. A 75, 060102 (R) (2007)], and while we disagree with their criticisms, we acknowledge them for giving us the opportunity to add…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
Friction is central to the motion of active (self-propelled) objects such as bacteria, animals, and robots. While in a viscous fluid friction is described by Stokes's law, objects in contact with other solid bodies are often governed by…
Can the laws of physics be unified. One of the most puzzling challenges is to reconcile physics and chemistry, where molecular physics meets condensed-matter physics, resulting from the scaling effect and dynamic fluctuation of glassy…
In view of the wide success of molecular quasi-chemical theory of liquids, this paper develops the soft-cutoff version of that theory. This development has important practical consequences in the common cases that the packing contribution…