Microfabricated integrated circuits revolutionized computation by vastly reducing the space, labor, and time required for calculations. Microfluidic systems hold similar promise for the large-scale automation of chemistry and biology, suggesting the possibility of numerous experiments performed rapidly and in parallel, while consuming little reagent. While it is too early to tell whether such a vision will be realized, significant progress has been achieved, and various applications of significant scientific and practical interest have been developed. Here a review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena. Specifically, this review explores the Reynolds number Re, addressing inertial effects; the Peclet number Pe, which concerns convective and diffusive transport; the capillary number Ca expressing the importance of interfacial tension; the Deborah, Weissenberg, and elasticity numbers De, Wi, and El, describing elastic effects due to deformable microstructural elements like polymers; the Grashof and Rayleigh numbers Gr and Ra, describing density-driven flows; and the Knudsen number, describing the importance of noncontinuum molecular effects. Furthermore, the long-range nature of viscous flows and the small device dimensions inherent in microfluidics mean that the influence of boundaries is typically significant. A variety of strategies have been developed to manipulate fluids by exploiting boundary effects; among these are electrokinetic effects, acoustic streaming, and fluid-structure interactions. The goal is to describe the physics behind the rich variety of fluid phenomena occurring on the nanoliter scale using simple scaling arguments, with the hopes of developing an intuitive sense for this occasionally counterintuitive world.

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Microfluidics: Fluid physics at the nanoliter scale

A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented DNA NN DG° 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used dif- ferent methods of data analysis; used different salt concen- trations; and presented the NN thermodynamics in different formats As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA poly- mers and oligomers Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies re- main Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics Empirical salt dependencies are also derived for oligonucleotides and polymers

/pdf/a-unified-view-of-polymer-dumbbell-and-oligonucleotide-dna-1r0s8psdu0.pdf

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

The binding specificities of RNA- and DNA-binding proteins are determined from experimental data using a ‘deep learning’ approach.

/pdf/predicting-the-sequence-specificities-of-dna-and-rna-binding-3h3zq9xxwi.pdf

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Synthetic molecular motors and mechanical machines.

DNA topoisomerases and their poisoning by anticancer and antibacterial drugs.

Conformational and Thermodynamic Properties of Supercoiled DNA

During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution of knot types produced by random cyclization of phage P4 DNA via its long cohesive ends. The simplest knots (trefoils) predominated, but more complex knots were also detected. The fraction of knots greatly diminished with decreasing solution Na+ concentration. By comparing these experimental results with computer simulations of knotting probability, we calculated the effective diameter of the DNA double helix. This important excluded-volume parameter is a measure of the electrostatic repulsion between segments of DNA molecules. The calculated effective DNA diameter is a sensitive function of electrolyte concentration and is several times larger than the geometric diameter in solutions of low monovalent cation concentration.

https://www.pnas.org/content/pnas/90/11/5307.full.pdf

Probability of DNA knotting and the effective diameter of the DNA double helix

Work in the 1990s has substantially increased our understanding of supercoiling conformations and energetics We now know many of the basic properties of supercoiled DNA as a result of the synergy between experimental and theoretical analyses We conclude by summarizing the results 1 All available data indicate a plectonemic structure for supercoiled DNA First, three types of EM (conventional, cryo, and scanning force) show the plectonemic form Second, the topology of the catenanes and knots generated from supercoiled DNA by the Int recombinase demands that the substrate supercoils are plectonemic, as does the topology of knotting by type-2 topoisomerases Third, all the theoretical and computer analyses indicate that the superhelix has the interwound form 2 The superhelix conformations are often branched, as observed using EM and Monte Carlo simulation Moreover, branching is required to explain the distribution of knots and catenanes produced by Int or topoisomerases as well as the dependence of s and Rg on sigma Branching frequency is very sensitive to sigma, DNA length, ionic conditions, DNA bends, and temperature Despite the qualitative agreement, the quantitative differences between experimental and computational data point out the need for further studies of branching 3 The results of Monte Carlo simulations, theoretical analyses, and cryo-EM show that the conformational and thermodynamic properties of supercoiled DNA depend strongly on ionic conditions The reason for such a dependence is clear Counterions shield DNA negative charges and decrease the repulsion of DNA segments in the tight interwound structure The effective double-helix diameter increases from 3 to 15 nm as the salt concentration is reduced from 100 to 001 M Experimental investigations of the dependence on ionic conditions of supercoiled DNA properties are just beginning The following conclusions refer to conditions of moderate to high monovalent or divalent ion concentrations (> or = 01 M [Na+] or > or = 001 M [Mg2+], respectively) 1 Wr takes up about 3/4 of the delta Lk, and Wr/delta Tw is independent of sigma for DNA > or = 25 kb in length A constant ratio is implied by the CD data, and Wr/delta Tw has been determined with conventional EM, cryo-EM, the Int topological method, and Monte Carlo simulation 2 The average number of supercoils is (08 to 09) x delta Lk and is independent of DNA length These results were obtained with EM, the Int topological method, and computer simulation(ABSTRACT TRUNCATED AT 400 WORDS)

Conformational and thermodynamic properties of supercoiled DNA.

Cloutier and Widom [Cloutier, T. E. & Widom, J. (2004) Mol. Cell 14, 355–362] recently reported that the cyclization efficiency of short DNA fragments, about 100 bp in length, exceeds theoretical expectations by three orders of magnitude. In an effort to resolve this discrepancy, we tried modifying the theory. We investigated how the distribution of the angles between adjacent base pairs of the double helix affects the cyclization efficiency. We found that only the incorporation of sharp kinks in the angle distribution provides the desired increase of the cyclization efficiency. We did not find a model, however, that fits all cyclization data for DNA fragments of different lengths. Therefore, we carefully reinvestigated the cyclization of 100-bp DNA fragments experimentally and found their cyclization efficiency to be in remarkable agreement with the traditional model of DNA bending. We also found an explanation for the discrepancy between our results and those of Cloutier and Widom.

https://www.pnas.org/content/pnas/102/15/5397.full.pdf

Cyclization of short DNA fragments and bending fluctuations of the double helix

Type II DNA topoisomerases catalyze the interconversion of DNA topoisomers by transporting one DNA segment through another. The steady-state fraction of knotted or catenated DNA molecules produced by prokaryotic and eukaryotic type II topoisomerases was found to be as much as 80 times lower than at thermodynamic equilibrium. These enzymes also yielded a tighter distribution of linking number topoisomers than at equilibrium. Thus, topoisomerases do not merely catalyze passage of randomly juxtaposed DNA segments but control a global property of DNA, its topology. The results imply that type II topoisomerases use the energy of adenosine triphosphate hydrolysis to preferentially remove the topological links that provide barriers to DNA segregation.

Alexander Vologodskii

Papers

Conformational and Thermodynamic Properties of Supercoiled DNA

Probability of DNA knotting and the effective diameter of the DNA double helix

Conformational and thermodynamic properties of supercoiled DNA.

Cyclization of short DNA fragments and bending fluctuations of the double helix

Simplification of DNA topology below equilibrium values by type II topoisomerases.