arXiv subjects

Walter Simmons

Publications and source records attributed to Walter Simmons.

6 recordsLinked to original sources

arXiv2015

Topology, Geometry, and Stability: Protein Folding and Evolution

The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows that features without length scales, i.e. topological features, are potentially of central importance. Topology is a natural mathematical tool for the study of shape and we avail ourselves of that tool to examine the relationship between the amino acid sequence and the shapes of protein molecules. We apply what we learn to conjectures about their biological evolution.

physics.bio-ph↗

arXiv2013

The Principle of Stationary Action in Biophysics: Stability in Protein Folding

Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action principle can be applied directly to study the stability of biological processes. The action principle in classical physics starts with the first variation of the action and leads immediately to the equations of motion. The second variation of the action leads in a natural way to powerful theorems that provide quantitative treatment of stability and focusing and also explain how some very complex processes can behave as though some seemingly important forces drop out. We first apply these ideas to the non-equilibrium states involved in two-state folding. We treat torsional waves and use the action principle to talk about critical points in the dynamics. For some proteins the theory resembles TST. We reach several quantitative and qualitative conclusions. Besides giving an explanation of why TST often works in folding, we find that the apparent smoothness of the energy funnel is a natural consequence of the putative critical points in the dynamics. These ideas also explain why biological proteins fold to unique states and random polymers do not. The insensitivity to perturbations which follows from the presence of critical points explains how folding to a unique shape occurs in the presence of dilute denaturing agents in spite of the fact that those agents disrupt the folded structure of the native state. This paper contributes to the theoretical armamentarium by directing attention to the logical progression from first physical principles to the stability theorems related to catastrophe theory as applied to folding. This can potentially have the same success in biophysics as it has enjoyed in optics.

physics.bio-ph↗

arXiv2011

Toward a Theory on the Stability of Protein Folding: Challenges for Folding Models

We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the progress from the random coil to the native state. In this paper we explore the stability of folding using established methods from physics and mathematics. Our result is a preliminary theory of the physics of folding. We suggest some tests of these ideas using folding simulations. We begin by supposing that folding events are related in some way to mechanical waves on the molecule. We adopt an analytical approach to the physics which was pioneered by M.V. Berry, (in another context), based upon mathematics developed mainly by R. Thom and V.I. Arnold. We find that the stability of the folding process can be understood in terms of structures known as caustics, which occur in many kinds of wave phenomena. The picture that emerges is that natural selection has given us a set of protein molecules which have mechanical waves that propagate according to several mathematically specific restrictions. Successful simulations of folding can be used to test and constrain these wave motions. With some additional assumptions the theory explains or is consistent with a number of experimental facts about folding. We emphasize that this wave-based approach is fundamentally different from energy-based approaches.

physics.bio-ph↗

arXiv2011

Physics of Caustics and Protein Folding: Mathematical Parallels

The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how energy from diverse small sources can drive a complex molecule to a unique state. We explore the possibility that the missing factor is in the geometry. A comparison of folding with other physical phenomena, together with analytic modeling of a molecule, led us to analyze the physics of optical caustic formation and of folding behavior side-by-side. The physics of folding and caustics is ostensibly very different but there are several strong parallels. This comparison emphasizes the mathematical similarity and also identifies differences. Since the 1970's, the physics of optical caustics has been developed to a very high degree of mathematical sophistication using catastrophe theory. That kind of quantitative application of catastrophe theory has not previously been applied to folding nor have the points of similarity with optics been identified or exploited. A putative underlying physical link between caustics and folding is a torsion wave of non-constant wave speed, propagating on the dihedral angles and $Ψ$ found in an analytical model of the molecule. Regardless of whether we have correctly identified an underlying link, the analogy between caustic formation and folding is strong and the parallels (and differences) in the physics are useful.

math-ph↗

arXiv2003

Direction Cryptography in Quantum Communications

We examine a situation in which an information-carrying signal is sent from two sources to a common receiver. The radiation travels through free space in the presence of noise. The information resides in a relationship between the two beams. We inquire into whether itis possible, in principle, that the locations of the transmitters can be concealed from a party who receives the radiation and decodes the information. Direction finding entails making a set of measurements on asignal and constructing an analytic continuation of the time dependent fields from the results. The fact that this process is generally different in quantum mechanics and in classical electrodynamics is the basis in this investigation. We develop a model based upon encoding information into a microscopic, transverse, non-local quantum image (whose dimensions are of the order of a few wavelengths) and using a detector of a type recently proposed by Strekalov et al. The optical system, which uses SPDC (Spontaneous Parametric Down Conversion), functions like a Heisenberg microscope: the transverse length, which encodes the signal information, is conjugate to the transverse momentum of the light. In the model, reading the signal information spoils the directional resolution of the detector, while determining the directions to the sources spoils the information content. Each beam, when examined in isolation, is random and indistinguishable from the background noise. We conclude that quantum communications can, in principle, be made secure against direction-finding, even from the party receiving the communication.

quant-ph↗

arXiv1996

Sonoluminescence in Neutron Stars

After a brief discussion of a possible relationship between the electroweak phase transition in highly compressed matter and gravitational collapse, we examine the speculative possibility that the electroweak phase transition might be contemporarily occurring in processes in neutron stars. We conjecture that adiabatic compression of neutron star matter due to focusing of the energy from a supernova bounce into a very small volume could result in extreme densities, and Fermi levels or temperature above $\cal{O}$ (100 GeV). We propose a qualitative scenario for sonoluminescence in neutron stars and discuss possible observable consequences.

astro-ph↗