Analysis of previously published sets DNA microarray gene expression data by singular value decomposition has uncovered underlying patterns or “characteristic modes” in their temporal profiles. These contribute unequally to the structure Moreover, essential features a given set profiles are captured using just small number characteristic modes. This leads striking conclusion that transcriptional response genome is orchestrated few fundamental change. both simple and robust, dominating...

Molecular dynamics techniques are used to study the microscopic aspects of several slow viscous flows past a solid wall, where both fluid and wall have molecular structure. Systems thousand molecules found exhibit reasonable continuum behavior, albeit with significant thermal fluctuations. In Couette Poiseuille flow liquids it is that no-slip boundary condition arises naturally as consequence roughness, velocity stress fields agree solutions Stokes equations. At lower densities slip appears,...

We report on molecular-dynamics simulations of the low--Reynolds-number flow Lennard-Jones fluids through a channel. Application pressure gradient to single fluid produces Poiseuille with no-slip boundary condition and Taylor-Aris hydrodynamic dispersion. For an immiscible two-fluid system we find (predictable) static contact angle and, when accelerated, velocity-dependent advancing receding angles. The approximate local velocity field is obtained, in which appears break down near line.

Significance Our focus is on a rich interdisciplinary problem touching earth science, hydrology, and statistical mechanics—an understanding of the statics dynamics network structures that we observe in fluvial landscape, their relation to evolution selection recurrent patterns self-organization. It an exemplar how diverse ideas, numerical simulation, elementary mathematics can come together help solve mystery ubiquitous pattern nature.

Significance Recently, evidence has been mounting that biological systems might operate at the borderline between order and disorder, i.e., near a critical point. A general mathematical framework for understanding this common pattern, explaining possible origin role of criticality in living adaptive evolutionary systems, is still missing. We rationalize apparently ubiquitous terms functional advantages. provide an analytical framework, which demonstrates optimal response to broadly different...

Since a fluid is composed of molecules, one always has the option calculating its static or dynamic properties by computing motion these constituents. For most purposes such procedure very inefficient, because it provides detailed information at molecular length scales, which are far beneath usual realm interest for continuum mechanics. There are, however, situations where microscopic details flow interesting if not crucial. example, fluids in geometries under high stress may exhibit...

We study the boundary conditions at a fluid-solid interface using molecular dynamics simulations covering broad range of interactions and fluid densities both simple chain-molecule fluids. The slip length is shown to be independent type flow, but rather related organization near solid, as governed by interactions.

Results of a renormalization-group analysis augmented by numerical calculations are presented for the electronic and phonon properties one-dimensional quasiperiodic lattice. Qualitative differences in band structure predicted analytically confirmed numerically. An exactly evaluated wave function shows power-law behavior. calculation diffusion coefficient also presented.

We describe the time evolution of gene expression levels by using a translational matrix to predict future genes based on their at some initial time. deduce for previously published DNA microarray data sets modeling them within linear framework characteristic modes obtained singular value decomposition. The resulting translation provides measure relationships among and governs evolution. show that truncated linking just few is good approximation full matrix. This finding suggests number...

We describe a method based on the principle of entropy maximization to identify gene interaction network with highest probability giving rise experimentally observed transcript profiles. In its simplest form, yields pairwise network, but it can also be extended deduce higher-order interactions. Analysis microarray data from genes in Saccharomyces cerevisiae chemostat cultures exhibiting energy metabolic oscillations identifies that reflects intracellular communication pathways adjust...

It is widely accepted that metabolic rates scale across species approximately as the 3/4 power of mass in most if not all groups organisms. Metabolic demand per unit thus decreases body increases. reflect both ability organism's transport system to deliver metabolites tissues and rate at which use them. We show ubiquitous law for interspecific scaling arises from simple, general geometric properties transportation networks constrained function biological The exponent other observed...

We show that a pair of chaotic systems subjected to the same noise may undergo transition at large enough amplitude and follow almost identical trajectories with complete insensitivity initial conditions. An analytic argument is presented generic in potential evolving equilibrium through standard Langevin dynamics collapse into trajectory long times.

We present a simple physical model that demonstrates the native-state folds of proteins can emerge on basis considerations geometry and symmetry. show inherent anisotropy chain molecule, geometrical energetic constraints placed by hydrogen bonds sterics, hydrophobicity are sufficient to yield free-energy landscape with broad minima even for homopolymer. These correspond marginally compact structures comprising menu choose from house their native states in. Our results provide general...

It has been known for decades that the metabolic rate of animals scales with body mass an exponent is almost always <1, >2/3, and often very close to 3/4. The 3/4 emerges naturally from two models resource distribution networks, radial explosion hierarchically branched, which incorporate a minimum specific details. Both show 2/3 if velocity flow remains constant, but can attain maximum value its exponent, 1/12. Quarter-power scaling arise even when there no underlying fractality....

Abstract The role of species interactions in controlling the interplay between stability ecosystems and their biodiversity is still not well understood. ability ecological communities to recover after small perturbations abundances (local asymptotic stability) has been studied, whereas likelihood a community persist when conditions change (structural received much less attention. Our goal understand effects diversity, interaction strengths network structure on volume parameter space leading...

A new equilibrium characterization of the spin-glass-paramagnet transition is presented. It based on size dependence sensitivity free energy to boundary conditions. Results numerical studies a three-dimensional Heisenberg spin-glass at $T=0$ are consistent with an algebraic decay this and suggest zero-temperature phase transition.