Main interests: Electron theory of metals (1955-1970, predicted cyclotron
resonance, Hofstadter butterfly), DNA thermodynamics (1970-1980), mesoscopics
(1980-1995, derived 2D Landauer dormula, giant conductance fluctuations,
predicted 3D quantum Hall), mortality and microevolution (1995-present,
phenomenological theory of survival in changing nvironment. Concept
of invariance is applied to mortality studies. Invariance implies
symmetry to specified transformations. Symmetry yields an exact "conservation
law" of the nvariant survival, because complexity leads to invariance
to an unspecified number of unquantified variables describing the population
and environment. The invariant probability to survive to a given age depends
on the infant mortality only. The dependence is piecewise linear, independent
of population, its life history and living conditions. The intersections
are simultaneous for an entire population of any age. I plan to discuss
physical and biological implications of this law, which agrees with all
experimental data for humans and flies, and which I argue may be universal).
My background is in biophysics, having recently finished graduate work
at the University of Michigan. The majority of my thesis was theoretical
and computational approach to protein structure designability; that
is, attempting to understand the physics of why some protein structures
could be easier to design or more frequent in the biological database.
My research interest and the drive behind participating in this workshop
is to learn more about the interplay of evolution in biomolecular folding,
structure, and function, with particular attention to genetic networks.
With a training in theoretical condensed matter and mathematical/statistical
physics I have been concentrating on problems inspired by molecular biology
and bioinformatics in the last years. My main research areas have been
the statistics of sequence alignment and RNA secondary structure formation.
During the workshop I hope to discuss these sort of problems with a large
variety of people and learn more about other areas of biology which pose
interesting questions amenable to the methods of statistical physics.
Emily S.C. Ching is trained as a theoretical physicist and her research interests are non-equilibrium nonlinear systems. In particular, she has been working on fluid turbulence. In turbulent flows, physical quantities such as velocity, pressure and temperature, display irregular fluctuations both in time and in space. The two key issues in the fundamental studies of turbulence are (i) to make sense of these complex fluctuations, and (ii) to understand the intermittent nature of turbulence and why dimensional agruments of the kind proposed by Kolmogorov are not exactly correct. Ching attempts to tackle these problems using a mixture of systematic theory, phenomenology and analyses of experiments. She has developed a formalism that characterizes the probability distribution of fluctuating quantities in terms of conditional averages. Interesting general features of the conditional averages of various turbulent quantities have been discovered in different turbulent flows.
By participating in the ITP program on statistical physics and biological
information, Ching would like to learn about the state-of-the-art analyses
of the large amount of biological data generated recently. Especially,
she hopes to be able to make use of her experience of analyses of complex
turbulent data to try to unravel biologically relevant knowledge from data
such as DNA and amino-acid sequences.
My background and training are in theoretical physical chemistry, soft
condensed matter physics, and applied mathematics. Among my interests are
the physical mechanisms of bioenergetics, transport, and cellular/subcellular
structure. I am particularly keen on learning new mathematical ways of
describing protein structure and genetic regulation.
My main current interest is DNA expression analysis (for details see
our website and PNAS article). My other possibly relevant field of interest
is protein folding.
My general research fields are statistical physics of disordered systems
and of system far from equilibrium. During the past few years, I began
to work also on topics related to biological evolution. May main
interests in this context are
- coevolution
- networks (species networks as well as genetic networks)
- different levels of organization (spatial patterns, group formation,
the role of large-scale structure)
- the evolutionary role of transpositions and other mutations which
are more complicated than point mutations.
I hope to learn more about biology and about models for evolution at
this workshop; I am also looking forward to meeting interesting people
and having some good discussions - one or two of which hopefully lead to
collaborations.
Previous interest:
Mesoscopic quantum physics (weak localization and Kondo
effect in quantum dots), quantum chaos, random matrix theory
Current interest:
1. Sequence-specific mechanical properties of RNA/DNA,
specifically: force-induced denaturation of RNA
2. Protein-DNA interaction
I am interested in all the mechanisms and molecules that are related to the origin of messenger RNA translation. In particular, as far as the origin of the genetic code is concerned, attempts have been made to falsify the proposed theories and thus identify the coevolution hypothesis as the one that best seems to capture the observations. Analysis of ß-sheets of proteins has identified the main adaptive theme that promoted the origin of genetic code organisation. I have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. This analysis seems to suggest that the historical factors played a leading role in forging the genetic code organisation. Recently, I have presented evidence that the late stage of genetic code structuring took place at a high temperature. The tRNA molecule is hypothesised to have originated by means of the direct duplication of an ancient gene codifying for a hairpin structure, and a non-monophyletic origin has been suggested for this molecule. Moreover, a model has been proposed for the origin of protein synthesis which hypothesises that the interaction between two hairpin RNA structures charged with amino acids was essential to the evolution of this process. Whereas the aminoacyl-tRNA synthetases were placed, according to their class, in an evolutionary relationship with either the proteins intervening in nonribosomal synthesis of peptide antibiotics or with the family of glutamine amidotransferases. I have also presented a model for the origin of the enzyme-coenzyme complex. This model is essentially based on an intermediate formed by a tRNA-like molecule covalently linked to a polypeptide. Thus, the model attributes the majority of the catalytic role in the ribonucleoprotein world to the latter complex and, in doing this, it takes into account the birth of the key intermediary in the origin of protein synthesis, namely peptidyl-tRNA, which would have otherwise been extremely difficult to select.
Key words: Origin of life - RNA world - Origin of translation - Genetic
code origin - Protein synthesis origin - tRNA origin - Last Universal Common
Ancestor - Aminoacy-tRNA synthetases
I have worked on problems in pattern formation (e.g. snowflake growth),
polymers (e.g. gelation/vulcanisation), statistical physics (e.g.
turbulence, liquid crystals, phase transition kinetics), condensed
matter physics (e.g. high temperature superconductivity) and mathematical
physics (e.g. global asymptotics, singularity formation). During
this program, I want to understand what biological information is,
what biological constraints can be used in conjunction with genome sequences
to understand gene expression, and whether algorithm heuristics motivated
by statistical physics can be of biological value.
Previous interest:
1. 3D Ising model, see Chaos and Order in Nature, ed. by H.
Haken, Springer-Verlag, 1981.
2. Non-equilibrium statistical physics, see Physics Reports,
118 (1985)1-131.
3. Books, see Chaos (1984, 1990), Elementary Symbolic Dynamics
and Chaos in Dissipative Systems (1989), Applied Symbolic Dynamics and
Chaos (1998), all published by World Sceintific
Current interest:
1. Avoided and under-represented strings in bacterial complete
genomes
2. Prokaryote phylogeny based on complete genomes
3. Repeated sequences in prokaryote complete genomes
I have a PhD on the Statistical Physics of Polymers from the University of Cambridge UK (1986-89). I held post-doc positions in France at Strasbourg (1989-90) and Saclay (1990-92). I was a Royal Society Research Fellow at the University of Sheffield (1992-95). Since 1995 I have had a tenured position in the School of Biological Sciences at the University of Manchester. I am Course Director for the MSc in Bioinformatics. I also teach evolutionary biology and genetics at undergraduate level. Details of Bioinformatics research and teaching at Manchester are available at http://bioinf.man.ac.uk.
I am currently working in the following areas.
1. RNA structure and evolution. Selection for thermodynamically stable
secondary structures in molecules such as ribosomal RNA and transfer RNA
has effects on the properties of the sequences and their rates of evolutionary
change.
2. Phylogenetic methods. We are developing methods for construction
of phylogenetic trees from molecular sequences using maximum likelihood
and Markov chain Monte Carlo methods. We are particularly interested in
applications to RNA phylogenies.
3. We are developing a relational database for comparative genome analysis.
This will allow systematic study of genome evolution (gene duplications,
losses and rearrangements), comparison of codon usage between organisms
and between genes, and comparison of rates of evolution of different genes.
4. Together with A McKane and B Drossel, also at this ITP meeting,
I have been working on the Webworld model of the evolution of multi-species
communities. The model generates foodweb structures for sets of many interacting
species and considers the the short term population dynamics (predator-prey
equations) and the long term evolutionary dynamics (speciations and extinctions).
I will be at ITP from April-June. I look forward to starting new research
collaborations. If anyone has any suggestions for work we can do together,
please e-mail me before then: Paul.Higgs@man.ac.uk.
My general background is in nonequilibrium statistical physics. In the past, I have worked mostly on nonequilibrium phenomena at surfaces, such as growth and electromigration. Recently I have moved away from generic models, such as the celebrated Kardar-Parisi-Zhang theory, towards the microscopic kinetic processes occurring at real crystal surfaces, e.g. in- and interlayer diffusion and two-dimensional nucleation. A second field of recent activity is driven single-file transport in lattice gases and cellular automata, with applications to traffic flow.
I also have a long standing but largely dilettante interest in biological
evolution, which has so far resulted in some preliminary work on quasispecies
dynamics. I come to Santa Barbara to learn about current developments in
molecular biology, notably in protein folding and related areas, in the
hope of picking up some interesting kinetic or statistical problems that
I might work on in the future.
WHO am I. b. HK 1941. BSc Nat'l Taiwan U 1963. PhD McGill 1969. Chalk River Labs. Ontario Canada 1969-1993. Chair, Nat'l Chung Hsing U 1993-1995. Professor, Phys Dept, Nat'l Central U 1995-present; joint appointment at Life Sci. Dept 2000-present.
WHAT I do. Prior to 1996: nucl phys, many-body, part. phys, quantum
field theory, quantum group/algebra and exactly solvable models. 1996-97,
complexity. From 1997 on: computational biology/bioinformatics. In
particular:
Biosequences - http://www.phy.ncu.edu.tw/hclee/SURE/reprints/hao00.pdf
Protein folding - http://www.phy.ncu.edu.tw/hclee/SURE/reprints/hcl00a.pdf
- http://www.phy.ncu.edu.tw/hclee/SURE/reprints/hcl00b.pdf
- http://www.phy.ncu.edu.tw/hclee/preprints/hpg.pdf
DNA uptake system in human pathogens - http://www.phy.ncu.edu.tw/hclee/preprints/uss1.pdf
mol. evolution - http://www.phy.ncu.edu.tw/hclee/preprints/oligo1.pdf
E-mail: hclee@phy.ncu.edu.tw
My background is in theoretical condensed matter physics. Till now,
my research has focused on issues related to the morphology of soft matter
systems such as the shape of droplets on patterned substrates or shape
instabilities of highly charged helium bubbles. I'm interested in applying
methods and techniques of soft matter physics to biological systems.
I am a 6th year graduate student in the physics department at Harvard
and a Graduate Fellow at the ITP. My training is in theoretical soft
condensed matter physics (e.g. polymers and colloids) and statistical physics;
while at Harvard I have worked with David Nelson on several biologically
inspired problems. In collaboration with an experimental biophysics,
I have looked at the dynamics of polymers threaded through narrow pores.
Under the influence of an electric field, single-stranded polynucleotides
can be driven through biological pores; we sought to understand what determines
their distribution of passage times. More recently, I have been interested
in single molecule micromanipulation experiments (in which, for example,
beads are attached to a polymer and used to pull on it), especially in
the presence of quenched randomness. In particular, we have obtained results
on the mechanical denaturantion of DNA with a random based sequence.
I mainly work on disordered systems: the protoptypes in the field are spin glasses, that are materials that are maybe not so interesting in themselves, but have the merit of having started a quantitative study of disordered systems. Numerical simulations are a technique of choice for studying this kind of materials, but the very complex free energy landscape of these systems makes the task very difficult to accomplish. Because of that I have been using and trying to improve Optimized Monte Carlo methods, that are also very needed when studying, for example, protein folding.
The most relevant physics question connected to this issues is about if realistic, finite dimensional spin glass like systems behave like the analytic solution of the mean field theory or not.
A different activity we just started recently is based on explicitely finding T=0 ground states of disordered systems. In this way one avoids the slowing down of the numerical simulations. I have recently been doing work on the connection among the T=0 results and the T>0 landscape.
I have also recently worked analyzing the dynamical behavior of these
very complex systems: I have tried to determine, for example, the scaling
laws governing the (potentially different) time scales of the process.
My early research was mainly in the application of field theory ideas to statistical mechanics, for instance renormalization group methods and the use of instantons to describe rare fluctuations and the asymptotic nature of perturbation expansions. Later my interests turned to non-equilibrium statistical mechanics, and I have recently used similar techniques to investigate topics such as stochastic ratchets, state selection and the coarse-graining of partial differential equations.
My background in non-equilibrium systems naturally led me to develop
an interest in the modelling of ecological systems. Recent work includes:
a model of food web dynamics which describes processes on both ecological
and evolutionary time scales, a model of a species-rich ecological community
which makes predictions about the species abundance distribution
and other generic features of ecosystems, and the use of a continuous
form of the Lotka-Volterra competition equations to investigate character
displacement and competitive speciation.
I'd like to meet people at the workshop with different backgrounds and
approaches to ecological modelling, and to come away with a better understanding
and appreciation of other modelling philosophies.
Background- primarily statistical physics
Directions of interest: Equilibrium and dynamics of single chain macromolecules, unconfined and confined, Effect of evolutionary models on current distribution and associations of biomolecules Tracking information flow through hierarchy of levels between molecular and organism populations
Reason for participation: to get better intuitive grasp of characteristics and dynamics of molecularly based complex biosystems
accompanied by: Ora E. Percus
Background- combinatorics, probability, and statistics
Directions of interest: Combinatorial and applied probability problems arising in molecular biology
Reason for participation: to get helpful biologicak background
In the past few years I have been interested in the analysis of DNA
sequences to detect short- or long-ranged correlations. Coding regions
of the DNA in all organisms have a universal short-range correlation: there
is a marked 3-base periodicity. This periodicity is most easily detected
via the Fourier transform and shows up as a sharp peak in the power spectrum.
We use this feature in a in-silico gene detection technique, GeneScan,
which is an ab inito or non consensus method for locating genes. My current
research focuses on the uses of different correlation-function based methods
in order to identify biologically significant features (genes, repeats,
etc.) on genomic DNA.
Originally physicist (electronics). 30 years doing biology, but with
physical mind setting. Currently mostly involved with genomic sequence
codes, protein structure and reconstruction of the earliest stages of evolution.
Contributions to: Origin and evolution of the triplet code, Stages of protein
evolution, Loop structure of proteins, Molecular theory of fast adaptation
(tuning function of tandem repeats), Multiple overlapping codes, Chromatin
code, DNA shape code (sequence-dependent DNA curvature and writhe), Translation
framing code, Genome units, combinatorial fusion theory of genome evolution,
Linguistic complexity.
Would like to take home updates on: complexity, chirality, prebiotic
chemistry, pattern recognition, signal processing, time series.
Hobbies: story teller, drinking parties, bird watching, mushrooms,
quiet music.
Experiences: Leningrad siege, Gulag, Siberia, Dissident and Jewish
movement in Russia, 24 years in Israel.