@article{jayaraman_hall_genzer_2007, title={Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration}, volume={127}, ISSN={["1089-7690"]}, DOI={10.1063/1.2787618}, abstractNote={We use lattice Monte Carlo simulations to study the thermodynamics of hybridization of single-stranded “target” genes in solution with complementary “probe” DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8–24 segments. The segments on the probe and target are distinct, with each segment representing a sequence of nucleotides that interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how surface density (number of probes per unit surface area) and concentration of target molecules affect the extent of hybridization. For short probe lengths, as the surface density increases, the probability of binding long stretches of target segments increases at low surface density, reaches a maximum at an intermediate surface density, and then decreases at high surface density. Furthermore, as the surface density increases, the target is less likely to bind completely to one probe; instead, it binds simultaneously to multiple probes. At short probe lengths, as the target concentration increases, the fraction of targets binding completely to the probes (specificity) decreases. At long probe lengths, varying the target concentration does not affect the specificity. At all target concentrations as the probe length increases, the fraction of target molecules bound to the probes by at least one segment (sensitivity) increases while the fraction of target molecules completely bound to the probes (specificity) decreases. This work provides general guidelines to maximizing microarray sensitivity and specificity. Our results suggest that the sensitivity and specificity can be maximized by using probes 130–180 nucleotides long at a surface density in the range of 7×10−5–3×10−4probemoleculespernm2.}, number={14}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Jayaraman, Arthi and Hall, Carol K. and Genzer, Jan}, year={2007}, month={Oct} }
 @article{jayaraman_santiso_hall_genzer_2007, title={Theoretical study of kinetics of zipping phenomena in biomimetic polymers}, volume={76}, ISSN={["1550-2376"]}, DOI={10.1103/physreve.76.011915}, abstractNote={In this work we use theory to obtain a mathematical expression for a time correlation function c(l,t) that provides insight into the zipping phenomena along a polymer going through a conformational transition. The polymer is modeled as an Ising-like chain with each segment being in one of two states: bound (+1) or unbound (-1). The time correlation function c(l,t) predicts the correlation between the state of the jth polymer segment at time 0 and the state of the (j+/-l)th polymer segment at time t . The expressions for c(0,t) , c(1,t), and c(2,t) obtained from our theory are dependent on the values of k0 and k1, where 2k0 is the rate coefficient for one segment changing from an unbound state to a bound state when both the neighboring segments are in an unbound state, and 2k1 is the rate coefficient for one segment changing from an unbound state to a bound state when both the neighboring segments are in a bound state. The ratio k1/k0 is an indication of the extent of cooperativity of binding adjacent segments on the polymer. We observe that c(0,t), c(1,t), and c(2,t) decay to 0 (no correlation) more slowly and the maximum values of c(1,t) and c(2,t) are lower for low values of k1/k0 as compared to high values of k1/k0. This is because at low values of k1/k0 the consecutive binding of adjacent segments along the polymer occurs slowly, while at high values of k1/k0 the cooperativity of binding adjacent segments is high and the segments along the polymer bind in a fast zipping mechanism.}, number={1}, journal={PHYSICAL REVIEW E}, author={Jayaraman, Arthi and Santiso, Erik E. and Hall, Carol K. and Genzer, Jan}, year={2007}, month={Jul} }
 @article{jayaraman_hall_genzer_2006, title={Computer Simulation Study of Molecular Recognition in Model DNA Microarrays}, volume={91}, ISSN={0006-3495}, url={http://dx.doi.org/10.1529/biophysj.106.086173}, DOI={10.1529/biophysj.106.086173}, abstractNote={DNA microarrays have been widely adopted by the scientific community for a variety of applications. To improve the performance of microarrays there is a need for a fundamental understanding of the interplay between the various factors that affect microarray sensitivity and specificity. We use lattice Monte Carlo simulations to study the thermodynamics and kinetics of hybridization of single-stranded target genes in solution with complementary probe DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8-24 segments. The segments on the probe and target are distinct and each segment represents a sequence of nucleotides ( approximately 11 nucleotides). Each probe segment interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how the probe length, temperature, or hybridization energy, and the stretch along the target that the probe segments complement, affect the extent of hybridization. For systems containing single probe and single target molecules, we observe that as the probe length increases, the probability of binding all probe segments to the target decreases, implying that the specificity decreases. We observe that probes 12-16 segments ( approximately 132-176 nucleotides) long gave the highest specificity and sensitivity. This agrees with the experimental results obtained by another research group, who found an optimal probe length of 150 nucleotides. As the hybridization energy increases, the longer probes are able to bind all their segments to the target, thus improving their specificity. The hybridization kinetics reveals that the segments at the ends of the probe are most likely to start the hybridization. The segments toward the center of the probe remain bound to the target for a longer time than the segments at the ends of the probe.}, number={6}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Jayaraman, Arthi and Hall, Carol K. and Genzer, Jan}, year={2006}, month={Sep}, pages={2227–2236} }
 @article{striolo_jayaraman_genzer_hall_2005, title={Adsorption of comb copolymers on weakly attractive solid surfaces}, volume={123}, ISSN={["1089-7690"]}, DOI={10.1063/1.1993557}, abstractNote={In this work continuum and lattice Monte Carlo simulation methods are used to study the adsorption of linear and comb polymers on flat surfaces. Selected polymer segments, located at the tips of the side chains in comb polymers or equally spaced along the linear polymers, are attracted to each other and to the surface via square-well potentials. The rest of the polymer segments are modeled as tangent hard spheres in the continuum model and as self-avoiding random walks in the lattice model. Results are presented in terms of segment-density profiles, distribution functions, and radii of gyration of the adsorbed polymers. At infinite dilution the presence of short side chains promotes the adsorption of polymers favoring both a decrease in the depletion-layer thickness and a spreading of the polymer molecule on the surface. The presence of long side chains favors the adsorption of polymers on the surface, but does not permit the spreading of the polymers. At finite concentration linear polymers and comb polymers with long side chains readily adsorb on the solid surface, while comb polymers with short side chains are unlikely to adsorb. The simple models of comb copolymers with short side chains used here show properties similar to those of associating polymers and of globular proteins in aqueous solutions, and can be used as a first approximation to investigate the mechanism of adsorption of proteins onto hydrophobic surfaces.}, number={6}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Striolo, A and Jayaraman, A and Genzer, J and Hall, CK}, year={2005}, month={Aug} }
 @article{jayaraman_hall_genzer_2005, title={Computer simulation study of pattern transfer in AB diblock copolymer film adsorbed on a heterogeneous surface}, volume={123}, ISSN={["1089-7690"]}, DOI={10.1063/1.2043048}, abstractNote={In this work we investigate how a pattern imposed in a copolymer film at a certain distance from the surface propagates through the film onto an adsorbing heterogeneous surface. We bias the copolymer film to adopt a specified target pattern and then use simulation to design a surface pattern that helps the adsorbed film to maintain that target pattern. We examine the effect of varying the copolymer chain length, the size of the target pattern, and the distance from the surface where the target pattern is applied, z′, on the extent of pattern transfer. For each chain length, target pattern, and z′ we compare the energy of the system when a pattern is applied in the bulk to the energy when no pattern is applied in order to understand why a certain pattern size is transferred to the surface with higher fidelity than the others. At constant chain length, pattern transfer is best when the pattern size brings the energy of the system close to the energy when no pattern is applied. At constant pattern size, pattern transfer is best in the systems with longer chains. This is because longer chains are more likely to adsorb as brushes and loops which then helps transfer the pattern through the adsorbed film down to the surface.}, number={12}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Jayaraman, A and Hall, CK and Genzer, J}, year={2005}, month={Sep} }
 @article{jayaraman_hall_genzer_2005, title={Designing pattern-recognition surfaces for selective adsorption of copolymer sequences using lattice Monte Carlo simulation}, volume={94}, ISSN={["1079-7114"]}, DOI={10.1103/physrevlett.94.078103}, abstractNote={We describe a simulation method to design surfaces for recognizing specific monomer sequences in copolymers. We fix the monomer sequence statistics of the AB copolymers on a surface containing two types of sites and allow the simulation to iterate towards an optimal surface pattern that can recognize and selectively adsorb the sequence in the copolymer. During the simulation the surface pattern is designed by switching identities of two randomly picked sites. For copolymers with less blocky sequences the designed surfaces recognize the correct sequence well when the segment-surface interactions dominate over the intersegment interactions. For copolymers with more blocky sequences recognition is good when the segment-surface interactions are only slightly stronger than the intersegment interactions.}, number={7}, journal={PHYSICAL REVIEW LETTERS}, author={Jayaraman, A and Hall, CK and Genzer, J}, year={2005}, month={Feb} }