A key aim of postgenomic biomedical research is to systematically catalogue all molecules and their interactions within a living cell. There is a clear need to understand how these molecules and the interactions between them determine the function of this enormously complex machinery, both in isolation and when surrounded by other cells. Rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize our view of biology and disease pathologies in the twenty-first century.

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Network biology: understanding the cell's functional organization

A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented, with emphasis on comparisons between theory and quantitative experiments. Examples include patterns in hydrodynamic systems such as thermal convection in pure fluids and binary mixtures, Taylor-Couette flow, parametric-wave instabilities, as well as patterns in solidification fronts, nonlinear optics, oscillatory chemical reactions and excitable biological media. The theoretical starting point is usually a set of deterministic equations of motion, typically in the form of nonlinear partial differential equations. These are sometimes supplemented by stochastic terms representing thermal or instrumental noise, but for macroscopic systems and carefully designed experiments the stochastic forces are often negligible. An aim of theory is to describe solutions of the deterministic equations that are likely to be reached starting from typical initial conditions and to persist at long times. A unified description is developed, based on the linear instabilities of a homogeneous state, which leads naturally to a classification of patterns in terms of the characteristic wave vector q0 and frequency ω0 of the instability. Type Is systems (ω0=0, q0≠0) are stationary in time and periodic in space; type IIIo systems (ω0≠0, q0=0) are periodic in time and uniform in space; and type Io systems (ω0≠0, q0≠0) are periodic in both space and time. Near a continuous (or supercritical) instability, the dynamics may be accurately described via "amplitude equations," whose form is universal for each type of instability. The specifics of each system enter only through the nonuniversal coefficients. Far from the instability threshold a different universal description known as the "phase equation" may be derived, but it is restricted to slow distortions of an ideal pattern. For many systems appropriate starting equations are either not known or too complicated to analyze conveniently. It is thus useful to introduce phenomenological order-parameter models, which lead to the correct amplitude equations near threshold, and which may be solved analytically or numerically in the nonlinear regime away from the instability. The above theoretical methods are useful in analyzing "real pattern effects" such as the influence of external boundaries, or the formation and dynamics of defects in ideal structures. An important element in nonequilibrium systems is the appearance of deterministic chaos. A greal deal is known about systems with a small number of degrees of freedom displaying "temporal chaos," where the structure of the phase space can be analyzed in detail. For spatially extended systems with many degrees of freedom, on the other hand, one is dealing with spatiotemporal chaos and appropriate methods of analysis need to be developed. In addition to the general features of nonequilibrium pattern formation discussed above, detailed reviews of theoretical and experimental work on many specific systems are presented. These include Rayleigh-Benard convection in a pure fluid, convection in binary-fluid mixtures, electrohydrodynamic convection in nematic liquid crystals, Taylor-Couette flow between rotating cylinders, parametric surface waves, patterns in certain open flow systems, oscillatory chemical reactions, static and dynamic patterns in biological media, crystallization fronts, and patterns in nonlinear optics. A concluding section summarizes what has and has not been accomplished, and attempts to assess the prospects for the future.

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Pattern formation outside of equilibrium

An introductory review of the central ideas in the modern theory of dynamic critical phenomena is followed by a more detailed account of recent developments in the field. The concepts of the conventional theory, mode-coupling, scaling, universality, and the renormalization group are introduced and are illustrated in the context of a simple example---the phase separation of a symmetric binary fluid. The renormalization group is then developed in some detail, and applied to a variety of systems. The main dynamic universality classes are identified and characterized. It is found that the mode-coupling and renormalization group theories successfully explain available experimental data at the critical point of pure fluids, and binary mixtures, and at many magnetic phase transitions, but that a number of discrepancies exist with data at the superfluid transition of $^{4}\mathrm{He}$.

Theory of Dynamic Critical Phenomena

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

The phenomenon of Bose-Einstein condensation of dilute gases in traps is reviewed from a theoretical perspective. Mean-field theory provides a framework to understand the main features of the condensation and the role of interactions between particles. Various properties of these systems are discussed, including the density profiles and the energy of the ground-state configurations, the collective oscillations and the dynamics of the expansion, the condensate fraction and the thermodynamic functions. The thermodynamic limit exhibits a scaling behavior in the relevant length and energy scales. Despite the dilute nature of the gases, interactions profoundly modify the static as well as the dynamic properties of the system; the predictions of mean-field theory are in excellent agreement with available experimental results. Effects of superfluidity including the existence of quantized vortices and the reduction of the moment of inertia are discussed, as well as the consequences of coherence such as the Josephson effect and interference phenomena. The review also assesses the accuracy and limitations of the mean-field approach.

https://arxiv.org/pdf/cond-mat/9806038.pdf

Theory of Bose-Einstein condensation in trapped gases

Clonal populations of cells exhibit substantial phenotypic variation. Such heterogeneity can be essential for many biological processes and is conjectured to arise from stochasticity, or noise, in gene expression. We constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated. Both stochasticity inherent in the biochemical process of gene expression (intrinsic noise) and fluctuations in other cellular components (extrinsic noise) contribute substantially to overall variation. Transcription rate, regulatory dynamics, and genetic factors control the amplitude of noise. These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.

https://science.sciencemag.org/content/sci/297/5584/1183.full.pdf

Stochastic Gene Expression in a Single Cell

https://science.sciencemag.org/content/sci/265/5178/1599.full.pdf

Entropic elasticity of lambda-phage DNA

Gene expression is a stochastic, or “noisy,” process. This noise comes about in two ways. The inherent stochasticity of biochemical processes such as transcription and translation generates “intrinsic” noise. In addition, fluctuations in the amounts or states of other cellular components lead indirectly to variation in the expression of a particular gene and thus represent “extrinsic” noise. Here, we show how the total variation in the level of expression of a given gene can be decomposed into its intrinsic and extrinsic components. We demonstrate theoretically that simultaneous measurement of two identical genes per cell enables discrimination of these two types of noise. Analytic expressions for intrinsic noise are given for a model that involves all the major steps in transcription and translation. These expressions give the sensitivity to various parameters, quantify the deviation from Poisson statistics, and provide a way of fitting experiment. Transcription dominates the intrinsic noise when the average number of proteins made per mRNA transcript is greater than ≃2. Below this number, translational effects also become important. Gene replication and cell division, included in the model, cause protein numbers to tend to a limit cycle. We calculate a general form for the extrinsic noise and illustrate it with the particular case of a single fluctuating extrinsic variable—a repressor protein, which acts on the gene of interest. All results are confirmed by stochastic simulation using plausible parameters for Escherichia coli.

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Intrinsic and extrinsic contributions to stochasticity in gene expression

The statistical dynamics of a classical random variable that satisfies a nonlinear equation of motion is recast in terms of closed self-consistent equations in which only the observable correlations at pairs of points and the exact response to infinitesimal disturbances appear. The self-consistent equations are developed by introducing a second field that does not commute with the random variable. Techniques used in the study of the interacting quantum fields can then be employed, and systematic approximations can be obtained. It is also possible to carry out a "charge normalization" eliminating the nonlinear coupling in favor of a dimensionless parameter which measures the deviation from Gaussian behavior. No assumptions of spatial or time homogeneity or of small deviation from equilibrium enter. It is shown that previously inferred renormalization schemes for homogeneous systems were incomplete or erroneous. The application of the method to classical microscopic systems, where it leads from first principles to a coupled-mode description is briefly indicated.

Statistical Dynamics of Classical Systems

The influence of hydrodynamic interactions on the coarsening rate r of a mist of droplets combining through diffusive coalescence is examined in detail. For a sufficiently rarified mist, the competing LifshitzSlyozov or evaporation-condensation mechanism is dominant, but the volume fraction of precipitate actually produced in most off-critical quench experiments probably favors direct coalescence, When the minority phase is continuous, as in a quench at the critical concentration, surface-tension eA'ects lead to a crossover from r -t'" to r -t, where t is the time.

Eric D. Siggia

Papers

Stochastic Gene Expression in a Single Cell

Entropic elasticity of lambda-phage DNA

Intrinsic and extrinsic contributions to stochasticity in gene expression

Statistical Dynamics of Classical Systems

Late stages of spinodal decomposition in binary mixtures