2000 John C. Polanyi Award LectureMother Nature and the molecular Big Bang

2002 ◽  
Vol 80 (1) ◽  
pp. 1-24 ◽  
Author(s):  
RJ Dwayne Miller

Biological molecules are mesoscopic systems that bridge the quantum and classical worlds. At the single molecule level, there are often more than 1 × 104 degrees of freedom that are involved in protein-mediated processes. These molecules are sufficiently large that the bath coordinate convolved to the reaction at an active site is defined by the surrounding protein tertiary structure. In this context, the very interatomic forces that determine the active protein structures create a strongly associated system. Thus, the bath fluctuations leading to reactive crossings involve highly hindered motions within a myriad of local minima that would act to cast the reaction dynamics into the high viscosity limit appropriate to glasses. However, the time scales observed for biological events are orders of magnitude too fast to meet this anticipated categorization. In this context, the apparent deterministic nature of biological processes represents an enormous challenge to our understanding of chemical processes. Somehow Nature has discovered a molecular scaffolding that enables minute amounts of energy to be efficiently channeled to perform biological functions without becoming entrapped in local minima. Clearly, energy derived from chemical processes is highly directed in biological systems. To understand this problem, we must first understand how energy is redistributed among the different degrees of freedom and fully characterize the protein relaxation processes along representative reaction coordinates in relation to these dissipative processes. This paper discusses the development of new nonlinear spectroscopic methods that have enabled interferometric sensitivity to protein motions on femtosecond time scales appropriate to the very fastest motions (i.e., bond breaking or the molecular "Big Bang") out to the slowest relaxation steps. This work has led to the Collective Mode Coupling Model as an explanation of the required reduced dimensionality in biological systems. Within this model, the largest coupling coefficients of the reaction coordinate are to the damped inertial collective modes of the protein defined by the strongly correlated secondary structures. These modes act to guide the reaction along the correct seam(s) in an otherwise highly complex potential energy surface. The mechanism by which biological molecules have been able to harness chemical energy over meso-length scales represents the first step towards higher levels of organization. The new insight afforded by the collective mode mechanism may prove important in understanding this larger issue of scaling in biological systems.Key words: biodynamics, energy transduction, ultrafast spectroscopy, nonlinear spectroscopy, primary processes in biology.

1989 ◽  
Vol 22 (3) ◽  
pp. 239-326 ◽  
Author(s):  
Alfred R. Holzwarth

The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.


Author(s):  
Yasuhisa Abe ◽  
David Boilley ◽  
Quentin Hourdillé ◽  
Caiwan Shen

Abstract A new framework is proposed for the study of collisions between very heavy ions which lead to the synthesis of Super-Heavy Elements (SHE), to address the fusion hindrance phenomenon. The dynamics of the reaction is studied in terms of collective degrees of freedom undergoing relaxation processes with different time scales. The Nakajima-Zwanzig projection operator method is employed to eliminate fast variable and derive a dynamical equation for the reduced system with only slow variables. There, the time evolution operator is renormalised and an inhomogeneous term appears, which represents a propagation of the given initial distribution. The term results in a slip to the initial values of the slow variables. We expect that gives a dynamical origin of the so-called “injection point s” introduced by Swiatecki et al in order to reproduce absolute values of measured cross sections for SHE. A formula for the slip is given in terms of physical parameters of the system, which confirms the results recently obtained with a Langevin equation, and permits us to compare various incident channels.


2012 ◽  
Vol 102 (3) ◽  
pp. 505a
Author(s):  
Peter Salamon ◽  
Mariam Ghochani ◽  
James Nulton ◽  
Terrence G. Frey ◽  
Avinoam Rabinovitch ◽  
...  

A new qualitative conception of the detonation mechanism in condensed explosives has been developed on the basis of experimental and numerical modelling data. According to the conception the mechanism consists of two stages: non-equilibrium and equilibrium. The mechanism regularities are explosive characteristics and they do not depend on explosive charge structure (particle size, nature of filler in the pores, explosive state, liquid or solid, and so on). The tremendous rate of loading inside the detonation wave shock discontinuity zone ( ca. 10 -13 s) is responsible for the origin of the non-equilibrium stage. For this reason, the kinetic part of the shock compression energy is initially absorbed only by the translational degrees of freedom of the explosive molecules. It involves the appearance of extremely high translational temperatures for the polyatomic molecules. In the course of the translational-vibrational relaxation processes (that is, during the first non-equilibrium stage of ca. 10 -10 s time duration) the most rapidly excited vibrational degrees of freedom can accumulate surplus energy, and the corresponding bonds decompose faster than behind the front at the equilibrium stage. In addition to this process, the explosive molecules become electronically excited and thermal ionization becomes possible inside the translational temperature overheat zone. The molecules thermal decomposition as well as their electronic excitation and thermal ionization result in some active particles (radicals, ions) being created. The active particles and excited molecules govern the explosive detonation decomposition process behind the shock front during the second equilibrium stage. The activation energy is usually low, so that during this stage the decomposition proceeds extremely rapidly. Therefore the experimentally observed dependence of the detonation decomposition time for condensed explosives is rather weak.


2018 ◽  
Vol 62 (4) ◽  
pp. 575-582
Author(s):  
Francesco Raimondi ◽  
Robert B. Russell

Genetic variants are currently a major component of system-wide investigations into biological function or disease. Approaches to select variants (often out of thousands of candidates) that are responsible for a particular phenomenon have many clinical applications and can help illuminate differences between individuals. Selecting meaningful variants is greatly aided by integration with information about molecular mechanism, whether known from protein structures or interactions or biological pathways. In this review we discuss the nature of genetic variants, and recent studies highlighting what is currently known about the relationship between genetic variation, biomolecular function, and disease.


KronoScope ◽  
2014 ◽  
Vol 14 (1) ◽  
pp. 71-89 ◽  
Author(s):  
Ettore Minguzzi

Abstract This paper proposes a cosmological model that uses a causality argument to solve the homogeneity and entropy problems of cosmology. In this model, a chronology violating region of spacetime causally precedes the remainder of the Universe, and a theorem establishes the existence of time functions precisely outside the chronology violating region. This model is shown to nicely reproduce Augustine of Hippo’s thought on time and the beginning of the Universe. In the model, the spacelike boundary representing the Big Bang is replaced by a null hypersurface at which the gravitational degrees of freedom are almost frozen while the matter and radiation content is highly homogeneous and thermalized.


1987 ◽  
Vol 19 (1-2) ◽  
pp. 7-49 ◽  
Author(s):  
S. J. Opella ◽  
P. L. Stewart ◽  
K. G. Valentine

The three-dimensional structures of proteins are among the most valuable contributions of biophysics to the understanding of biological systems (Dickerson & Geis, 1969; Creighton, 1983). Protein structures are utilized in the description and interpretation of a wide variety of biological phenomena, including genetic regulation, enzyme mechanisms, antibody recognition, cellular energetics, and macroscopic mechanical and structural properties of molecular assemblies. Virtually all of the information currently available about the structures of proteins at atomic resolution has been obtained from diffraction studies of single crystals of proteins (Wyckoff et al, 1985). However, recently developed NMR methods are capable of determining the structures of proteins and are now being applied to a variety of systems, including proteins in solution and other non-crystalline environments that are not amenable for X-ray diffraction studies. Solid-state NMR methods are useful for proteins that undergo limited overall reorientation by virtue of their being in the crystalline solid state or integral parts of supramolecular structures that do not reorient rapidly in solution. For reviews of applications of solid-state NMR spectroscopy to biological systems see Torchia and VanderHart (1979), Griffin (1981), Oldfield et al. (1982), Opella (1982), Torchia (1982), Gauesh (1984), Torchia (1984) and Opella (1986). This review describes how solid-state NMR can be used to obtain structural information about proteins. Methods applicable to samples with macroscopic orientation are emphasized.


Author(s):  
R.G. Shulman

It was my pleasure to participate in Oleg’s 65th birthday celebration and to reminisce about the early days of Biochemical NMR. Oleg was always there. I remember in the summer in the early 1960s sitting on lawn chairs at a Gordon Conference and discussing the need for a meeting on biochemical NMR. This was to convene those with common interests, and out of this grew the 1964 meeting in Boston, which was the first International Conference on Magnetic Resonance in Biological Systems. In organizing the 1964 meeting Oleg was stalwart, in charge of the local arrangements at the old mansion, home of the American Academy of Arts and Sciences. The venue was much appreciated by the more than 100 attendees, and the smooth arrangements and elegant, although somewhat dowdy locale, contributed to the sense, generated by the meeting, that the field had a coherent scientific core and a meaningful future. In the early days of the 1960s the field of magnetic resonance in biological systems, brought together biannually by the society, had a coherence that was nurtured by the society. In those days the NMR and ESR methods were much less developed than they soon became, so that any reasonably competent spectroscopist could understand all the methods employed. Additionally, because the earlier studies concentrated upon the better understood biological molecules or processes, the breadth of the applications did not baffle a slightly informed biochemist. The rapid advances in definite understanding were thrilling to practitioners in the field, and individual efforts were motivated by a sense that the field was going to grow. By that time NMR was firmly established as a quantitative method in chemistry, solid state physics, and other material sciences so that with the results in hand it was logical to extrapolate to a future in which magnetic resonance could be central to biological research. These high hopes, however, required considerable confidence in extrapolation, because the individual findings were sometimes slight when compared to the exciting cutting edges of biological research.


2005 ◽  
Vol 13 (01) ◽  
pp. 23-30
Author(s):  
JUKKA TIENARI

An attempt is made for pedagogical purposes to construct a model as simple as possible for analyzing biochemical control mechanisms that participate in the selection of molecules in biological systems. The analysis is simplified by an assumption that the system is in a steady state. The mechanisms result from the principle that in an open system the absolute rate constants determine the proportions of components. Reactions producing or consuming substances that influence the rates of other reactions in the system also influence the amounts of participating substances. Reciprocal effects result in internal control which selects some substances by increasing their relative amounts. Similar mechanisms also control processes other than chemical reactions. The selection contributes to the maintenance of the non-random distribution of molecules in the biosphere that allows certain biological molecules to be more abundant than other molecules consisting of the same elements and having comparable standard free energies of formation.


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