- I was an undergraduate at Reed College, earning a BA degree in the dual major Physics and Mathematics, a graduate stu... moreI was an undergraduate at Reed College, earning a BA degree in the dual major Physics and Mathematics, a graduate student at The Rockefeller University, earning a PhD degree in Mathematical Physics, and a postdoctoral fellow of the Miller Institute for Research in Science at the University of California at Berkeley department of Physics. My entire academic career was experienced at The Georgia Institute of Technology where I was School Chairman, 1999-2005, and attained the rank of Regents' Professor of Physics Emeritus.edit
Incompatible theories for hydrodynamic fluctuations far from full equilibrium are described and compared. The two types of approach are compared with the well established near equilibrium theory of hydrodynamic fluctuations. They are also... more
Incompatible theories for hydrodynamic fluctuations far from full equilibrium are described and compared. The two types of approach are compared with the well established near equilibrium theory of hydrodynamic fluctuations. They are also checked for internal consistency and it is shown that one of the approaches checks out as inconsistent. The other approach is recommended as a valid approach.
This paper describes a new mathematical method called conflation for consolidating data from independent experiments that measure the same physical quantity. Conflation is easy to calculate and visualize and minimizes the maximum loss in... more
This paper describes a new mathematical method called conflation for consolidating data from independent experiments that measure the same physical quantity. Conflation is easy to calculate and visualize and minimizes the maximum loss in Shannon information in consolidating several independent distributions into a single distribution. A formal mathematical treatment of conflation has recently been published. For the benefit of experimenters wishing to use this technique, in this paper we derive the principal basic properties of conflation in the special case of normally distributed (Gaussian) data. Examples of applications to measurements of the fundamental physical constants and in high energy physics are presented, and the conflation operation is generalized to weighted conflation for cases in which the underlying experiments are not uniformly reliable.
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In this paper we review and extend our earlier recent work on thermostated systems. A description of nano-biological systems by Markov chains in coordinate space in the strongly overdamped limit is presented. Characterization of the most... more
In this paper we review and extend our earlier recent work on thermostated systems. A description of nano-biological systems by Markov chains in coordinate space in the strongly overdamped limit is presented. Characterization of the most probable path is given and a new formula for the probability of this special path is provided from recursion formulae. The deterministic limit is derived and the significance of Lagrange multipliers introduced when constructing the most probable path is elucidated. The characterization of the generation of path entropy by the most probable path is given an equivalent interpretation relating to the rate of entropy production by the most probable path. The paper concludes with an account of the biological implications. Here we address why the origin of life and its subsequent evolution took place, not the particular chemical details of how it happened.
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In 1990, two papers appeared [1, 2] in which it was shown that 1) there is a fundamental connection between the dynamics of fluctuations and chaos in macroscopic classical dissipative systems; and 2) this connection is paralleled in... more
In 1990, two papers appeared [1, 2] in which it was shown that 1) there is a fundamental connection between the dynamics of fluctuations and chaos in macroscopic classical dissipative systems; and 2) this connection is paralleled in quantum systems in the sense that the classical Lyapunov exponent is a quantum signature of classical chaos. Several examples of the amplification of intrinsic fluctuations by chaos in classical dissipative systems are given in support of 1). In support of 2), the quantum signature of ...
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An exact value for Avodagro's number, namely NA* = (84446888)^3, is proposed. The number 84446888 represents the side length of a cube of atoms whose volume is closest, among all integral side lengths, to the current official NIST... more
An exact value for Avodagro's number, namely NA* = (84446888)^3, is proposed. The number 84446888 represents the side length of a cube of atoms whose volume is closest, among all integral side lengths, to the current official NIST value of Avogadro's number. This value NA* is nearly dead center of the estimated range for the value of Avogadro's number, and is within the official standard level of uncertainty. Adoption of this value as the fixed value for NA would eliminate the current time-dependent definition of Avogadro's number, which depends on the definition of kilogram via an unstable physical artifact. It would also eliminate the need for the kilogram artifact altogether, since then, by definition, a kilogram would be exactly 1000/12 the mass of NA* atoms of carbon-12.
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Rectified Brownian motion provides a mechanistic alternative to the power stroke model for the function of motor proteins and other enzyme complexes. ATP is the source of metabolic free energy for motor proteins such as kinesin and myosin... more
Rectified Brownian motion provides a mechanistic alternative to the power stroke model for the function of motor proteins and other enzyme complexes. ATP is the source of metabolic free energy for motor proteins such as kinesin and myosin V. In the power stroke models, the energy of ATP hydrolysis causes chemo-mechanical energy conversion although the precise manner by which this occurs has yet to be identified. In the rectified Brownian motion model, the energy released by ATP hydrolysis causes an irreversible conformational switch in the ATP binding protein that results in release of the motor protein head from the track along which it moves, and Brownian motion provides the power for the head to move to a new binding site. Asymmetric boundary conditions for this diffusive motion result in a directed motion on the average.
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Abstract A wealth of research on stochastic resonance (SR) during the last decade has led to different ways of defining this phenomenon. Most prominent are measures based on the power spectrum and on the residence time distribution... more
Abstract A wealth of research on stochastic resonance (SR) during the last decade has led to different ways of defining this phenomenon. Most prominent are measures based on the power spectrum and on the residence time distribution function. Using a novel (fully systematic) theory for residence time distributions, we show that the measures for SR based on the residence time distribution introduced so far are ambiguous. In particular, we show that SR is-at least for weak signals-not a bona-fide resonance notwithstanding with recent ...
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At the nanometer scale, biological mechanisms are dominated by Brownian motion. On the nanosecond scale, Brownian motion inside cells manifests itself as diffusion. Utilizing metabolic energy, the cell is able to obtain useful work from... more
At the nanometer scale, biological mechanisms are dominated by Brownian motion. On the nanosecond scale, Brownian motion inside cells manifests itself as diffusion. Utilizing metabolic energy, the cell is able to obtain useful work from Brownian motion through a mechanism called rectified Brownian motion. This mechanism is distinct from that of Brownian ratchets. Rectified Brownian motion amounts to diffusion with asymmetric boundary conditions. This mechanism will be illustrated by the function of ubiquinone in electron transport chains, and by the action of the motor protein kinesin. Nanobiology shows us that rectified Brownian motion may be a useful component in the design of nanoscale devices.
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ABSTRACT
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We examine from fizst principles the effects of a stochastic pump on the output fluctuations of a laser. The Hamiltonian for a four-level molecule interacting with a stochastic semiclassical pump field and quantized laser field is used to... more
We examine from fizst principles the effects of a stochastic pump on the output fluctuations of a laser. The Hamiltonian for a four-level molecule interacting with a stochastic semiclassical pump field and quantized laser field is used to obtain density-matrix equations of motion. Noise from the pump field and from spontaneous emission is introduced systematically, as opposed to the ad hoc inclusion of random forces in the semiclassical equations. The relationship of this theory with previous quantum and semiclassical equations is described ...
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A modified mode-coupling theory is presented to explain discrepancies between measured values and theoretical predictions for thelong-time tail of the velocity-autocorrelation function of diffusing particles. The measurements of Paul and... more
A modified mode-coupling theory is presented to explain discrepancies between measured values and theoretical predictions for thelong-time tail of the velocity-autocorrelation function of diffusing particles. The measurements of Paul and Pusey and of Ohbayashi et al. areanalyzed and shown to be in much better agreement with theory than previously supposed, provided that the new, modified theory is used. The new theory regularizes spatial singularities in order to remove temporal singu-larities. In doing so, it provides a ...
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Numerical simulations of (1) using establishedtech-niques" for simulating stochastic differential equations fit the measured data very well. Using the parameters found this way, the contracted model can be... more
Numerical simulations of (1) using establishedtech-niques" for simulating stochastic differential equations fit the measured data very well. Using the parameters found this way, the contracted model can be mathematically analyzed to the point of producing formulas for the mean and the variance. These results agree with the measurements and the simulations to within the expected accura-cy.
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The basic concepts of nonequilibrium thermodynamics and biochemical energetics are brought together in an attempt to define sharply the problem of the origin of life. An analysis of the energetics of cellular metabolism requires two... more
The basic concepts of nonequilibrium thermodynamics and biochemical energetics are brought together in an attempt to define sharply the problem of the origin of life. An analysis of the energetics of cellular metabolism requires two fundamental distinctions. Firstly, one must distinguish between arbitrary systems, in which the time evolution is governed by the entropy, and thermally buffered systems, in which the time evolution is governed by the free energy. Secondly, one must distinguish between systems closed with respect to energy ...
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An elementary explanation is given for the boundary shadings observed in plots of chaotic attractors for the Feigenbaum map and the circle map. An explicit analytic representation of these phenomena is presented which provides the... more
An elementary explanation is given for the boundary shadings observed in plots of chaotic attractors for the Feigenbaum map and the circle map. An explicit analytic representation of these phenomena is presented which provides the location of the boundaries and which side of the boundaries is shaded. For the Feigenbaum map, the same analytic expressions also yield the U sequence
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Recent developments in the theory of nonequilibrium processes are discussed in the context of light-scattering experiments. The effects of thermal gradients in liquids on the Rayleigh-Brillouin scattering of laser light is discussed. Of... more
Recent developments in the theory of nonequilibrium processes are discussed in the context of light-scattering experiments. The effects of thermal gradients in liquids on the Rayleigh-Brillouin scattering of laser light is discussed. Of special interest is the emergence of long-range order effects 89 a consequence of the nonequilibrium state as compared with equilibrium. A discussion of wall effeds, which result from the finite size of the scattering chamber, is provided for the related problem of diffusion in thermal gradienta. In this ...
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Quantum chaos has been demonstrated in several studies of the interaction between N two-level quantum systems and a single-mode radiation field interacting in a resonant cavity. It has been shown that the mechanism for this chaos is... more
Quantum chaos has been demonstrated in several studies of the interaction between N two-level quantum systems and a single-mode radiation field interacting in a resonant cavity. It has been shown that the mechanism for this chaos is dynamically identicalto a periodically perturbed, near-separatrix motion of a pendulum. Identification of this mechanism followed from examination of the rotating-wave approximation and corrections to this approximation. Our earlier study established the nature of the corrections on the basis of numerical ...
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Up to now, I have tried to stay closely tied to experiments and observations. The following is not based directly on experiments. Some molecular modeling is used, and the underpinning is, of course, based on all the experimental evidence... more
Up to now, I have tried to stay closely tied to experiments and observations. The following is not based directly on experiments. Some molecular modeling is used, and the underpinning is, of course, based on all the experimental evidence behind what has been discussed up to now. The conceptual issues spoken about earlier need to be revisited here. "Chicken-egg" questions, IC, and initiation issues will be addressed from here onward by speculation, reasoning, theory in short, not experiment. In so far as real experiments will present themselves naturally as we proceed, the reader should make note of them. It is initiation that is the mysterium tremendum at this stage. Let us set the stage. The primordial soup is an energized chemical broth, vigorous with chemical ferment, driven by the Sun's UV radiation. Redox, thioester and pyrophosphate driven precursors to many contemporary biochemical processes are manifest. Thermal, wet/dry cycle niches abound on the surface of a ...
Uranya: I have tried to pursue the two base code idea a little further. To do so I have attempted to combine the table you drew based on Schimmel and Beebe's classification of aaRS's into sub-classes with the table of... more
Uranya: I have tried to pursue the two base code idea a little further. To do so I have attempted to combine the table you drew based on Schimmel and Beebe's classification of aaRS's into sub-classes with the table of complementary codons I drew based on the work of the Rodins'. I start by assuming that class Ia and IIa aaRS's correspond with the earliest aa's to be incorporated into the code. The aromatic aa's associated with class Ic and IIc aaRS's are surely later additions. However, the class Ib and IIb aa's, asp, asn, glu, gln and lys, seem not to be very late additions since asp and glu are prominent in abiotic syntheses of aa's and are important in making proteinoids. However, if we take the view that matters began with the C and G bases, and that A and U were incorporated sparingly at first, then we are forced to look at classes Ia and IIa first. With this in mind I have reordered your table as follows: To this list there corresponds a lis...
CGN)n for small n. We say this codes for poly-arginine because the reaction of the arginine phosphate with the ribose 2'-OH between C and G is greater than for other pairings with either a different amino acid or a different two base... more
CGN)n for small n. We say this codes for poly-arginine because the reaction of the arginine phosphate with the ribose 2'-OH between C and G is greater than for other pairings with either a different amino acid or a different two base codon. The work in Mike Yarus' lab shows a strong interaction between arginine and CGN sequences using SELEX. That is, SELEX finds an interaction between some amino acids and their contemporary codons. That's not a frozen accident. There is surely also a difference between simple binding of an amino acid to a codon sequence and esterification of the codon's ribosyl 2'-OH by an amino acyl phosphate. The Yarus experiments don't look at that. The translation from a nucleotide sequence to an amino acid sequence depends on a putative physical-chemical interaction between the amino acid and the nucleotide codons. At first there is a smaller list of amino acids involved than at present and as the mechanism evolves so does the coding. U:...
Probably the most basic form of energy on the primitive Earth was heat. Those many forms of synthesis that involve dehydrations are inhibited by the abundance of water. Simple heat can remove water by evaporation, greatly reducing the... more
Probably the most basic form of energy on the primitive Earth was heat. Those many forms of synthesis that involve dehydrations are inhibited by the abundance of water. Simple heat can remove water by evaporation, greatly reducing the inhibition. This process has the capacity to form polymers, as has been demonstrated with amino acids. Heat also can be transduced into chemical forms of energy as will be discussed below. The UV radiation from the Sun has been available as a source of energy since the time the Earth formed over four billion years ago. Much of this radiation is around 400 nm in wavelength and has enough energy per photon to promote oxidation of iron íµí°¹íµí± 2+ + íµí±íµí± ⟶ íµí°¹íµí± 3+ + íµí± − It has been known for a long time that íµí°» 2 is produced by irradiation of aqueous acid solutions of ferrous salts with UV (~250 nm). It is now known that this reaction occurs at neutral or even alkaline pH and does so more readily. Even up to 400 nm the quantum yield i...
Reynard: Thank you. You have a better chance to hear about good recent sources than I do. Tell me about what you have learned. U: First of all, a good recent source is the book The Aminoacyl-tRNA Synthetases, (Eds. Ibba, Francklyn and... more
Reynard: Thank you. You have a better chance to hear about good recent sources than I do. Tell me about what you have learned. U: First of all, a good recent source is the book The Aminoacyl-tRNA Synthetases, (Eds. Ibba, Francklyn and Cusack, Landes Bioscience, 2005). It has chapters about each amino acid aaRS as well as other chapters. Secondly there is a series of papers by Andrei Rodin and Sergei Rodin (and earlier with Susumu Ohno) that show codon patterns associated with the two classes. R: Are these Rodins the Rodin brothers? U: Andrei is Andrei Sergeyevich so I suspect he is the son, not the brother, of Sergei. R: I too have looked for patterns relating amino acids to their aaRS's. The results surprised me. The link [polymer biosynthesis] contains the excerpt below. The tRNA's contain anti-codons at one end that read the codons by anti-parallel base pairing. At the other end of the tRNA is the amino acid attachment site on the tRNA 3' terminus. The aaRS's cata...
Uranya: If you talk to almost any contemporary molecular biologist or biochemist they will tell you that the answers lie in the RNA World point of view. I know you have already explained where you think the RNA World arises during... more
Uranya: If you talk to almost any contemporary molecular biologist or biochemist they will tell you that the answers lie in the RNA World point of view. I know you have already explained where you think the RNA World arises during geophysical chemical evolution but tell me again the key points. Reynard: Okay. The main objection is that the typical RNA World argument is given out of context. Let that idea sink in! Instead, it is assumed that RNA's of every length are readily available. Clever mechanisms are often constructed using this material. In context, there is a highly energized (UV, redox, thioester, P~P) microsphere world with dividing compartments that are impermeable to polymers, even of short length (6 to 9 units). Initially the general context is an energized racemic polypeptide world with membranes and microspheres and replication by division of these compartments. Furthermore, RNA requires mononucleotides, as its monomers, and these monomers are dehydration condensa...
By way of review and as an exercise in molecular algebra, let us look at base pairing in more detail. The modern system uses two sets of base pairs, CG and UA. With these four bases, 64 three base codons can be made. However, it is... more
By way of review and as an exercise in molecular algebra, let us look at base pairing in more detail. The modern system uses two sets of base pairs, CG and UA. With these four bases, 64 three base codons can be made. However, it is possible that the coding began with only one base pair, say CG, the more thermodynamically stable of the two available (three hydrogen bonds instead of two). Both the base pairing processes and the primitive RNA translator function as already described. The smoothness or ease of this functioning is greatly enhanced if structures of one pure chirality are used. That RNA replication and translation are much smoother for a system of pure chirality than for a racemic system is not obviated by reduction from two base pair sets to just one set. So we will analyze a one base pair system based on CG. Uranya: The fact that the modern system uses two base pair sets is another example of felicity. The use of two sets depends on the "accident" that the shap...
Without energy inputs, the equilibrium thermodynamics for the mixture of molecular species on the primitive Earth leads to many biologically relevant small molecules but does not yield polymers. The primitive geophysical world does not... more
Without energy inputs, the equilibrium thermodynamics for the mixture of molecular species on the primitive Earth leads to many biologically relevant small molecules but does not yield polymers. The primitive geophysical world does not give rise to macromolecules of the type seen now in genetically directed protein biosynthesis enzyme (and ribozyme) complexes until energy is allowed to flow through this matter. UV, redox energy, reducing potential, thioesters and pyrophosphate are natural products of geophysically natural processes. This is the coupling Lipmann speaks about. Banded iron formations are a lasting signature of this naturalness. As argued above, this creates a world in which dehydrations can be promoted, in spite of the preponderance of water. Heat is also available to support production of dehydration bonds. So multimers, oligomers, small polypeptides, proto-coenzymes, and even mononucleotides can be expected in this developing primitive environment. Not polynucleotide...
The origin and evolution of the Universe is surely the age old problem that for millennia has fascinated thinking persons. That life could arise and develop to the point of thinking, reasoning creatures is an aspect of the larger problem... more
The origin and evolution of the Universe is surely the age old problem that for millennia has fascinated thinking persons. That life could arise and develop to the point of thinking, reasoning creatures is an aspect of the larger problem that has caused special fascination. This means that the Universe has reached the stage where it contemplates itself. It also means it is able to fashion machines that can leave this Earth and land on the Moon, and then return, all the while carrying a few of these living, thinking creatures. How splendidly amazing this circumstance is! In the following paragraphs, I will focus on that aspect of the broader problem we call life. Specifically, I will focus on the origin and evolution of molecular genetics, i.e. the genetic code and its associated protein biosynthesis machinery. This topic is especially interesting because mankind has learned a very great deal about it during the last hundred years and because certain conceptual issues remain unresolv...
In the context we have developed here, the origin of tRNA is intimately tied to the origin of aaRS's. What good would the aaRS's be if there were no tRNA's for them to service? So, tRNA's emerge first.? Propagating racemic... more
In the context we have developed here, the origin of tRNA is intimately tied to the origin of aaRS's. What good would the aaRS's be if there were no tRNA's for them to service? So, tRNA's emerge first.? Propagating racemic proteinoid microsphere populations exhibit internal polymerizations of RNA and of pure chiral linear polypeptides. The spheres, ur-cells, are porous to the monomers but not to polymers of sufficient length. However, polymerization is uphill thermodynamically and kinetically constrained. These barriers are overcome by robust energy ur-metabolism culminating in strong, pyrophosphate driven polymerizations. These trapped polymers constitute the ur-genome and ur-proteinome. RNA strand propagation, catalyzed by an ur-polymerase that makes a complement of a complement that is equal to a replica, must keep pace with the ur-cell replication rate. Not all steps are uphill thermodynamically or are driven by a high P~P concentration. The self-assembly of micr...
Imagine that you get such certain awesome experience and knowledge by only reading a book. How can? It seems to be greater when a book can be the best thing to discover. Books now will appear in printed and soft file collection. One of... more
Imagine that you get such certain awesome experience and knowledge by only reading a book. How can? It seems to be greater when a book can be the best thing to discover. Books now will appear in printed and soft file collection. One of them is this book structure and motion membranes nucleic acids and proteins. It is so usual with the printed books. However, many people sometimes have no space to bring the book for them; this is why they can't read the book wherever they want.