arXiv subjects

Avraham Halperin

Publications and source records attributed to Avraham Halperin.

3 recordsLinked to original sources

arXiv2008

On the Adsorption of Two-State Polymers

Monte Carlo(MC) simulations produce evidence that annealed copolymers incorporating two interconverting monomers, P and H, adsorb as homopolymers with an effective adsorption energy per monomer, $ε_{eff}$, that depends on the PH equilibrium constants in the bulk and at the surface. The cross-over exponent, $Φ,$ is unmodified. The MC results on the overall PH ratio, the PH ratio at the surface and in the bulk as well as the number of adsorbed monomers are in quantitative agreement with this hypothesis and the theoretically derived $ε_{eff}$. The evidence suggests that the form of surface potential does not affect $Φ$ but does influence the PH equilibrium.

cond-mat.soft↗

arXiv2004

Hybridization Isotherms of DNA Microarrays and the Quantification of Mutation Studies

Background: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild type DNA. This excess can give rise to false positives due to competitive hybridization of the wild type target at the mutation spot. The analysis of the DNA array data is typically qualitative aiming to establish the presence or absence of a particular point mutation. Our theoretical approach yields methods for quantifying the analysis so as to obtain the ratio of concentrations of mutated and wild type DNA. Method: The theory is formulated in terms of the hybridization isotherms relating the hybridization fraction at the spot to the composition of the sample solutions at thermodynamic equilibrium. It focuses on samples containing an excess of single stranded DNA and on DNA arrays with low surface density of probes. The hybridization equilibrium constants can be obtained by the nearest neighbor method. Results: Two approaches allow us to obtain quantitative results from the DNA array data. In one the signal of the mutation spot is compared with that of the wild type spot. The implementation requires knowledge of the saturation intensity of the two spots. The second approach requires comparison of the intensity of the mutation spot at two different temperatures. In this case knowledge of the saturation signal is not always necessary. Conclusions: DNA arrays can be used to obtain quantitative results on the concentration ratio of mutated DNA to wild type DNA in studies of somatic point mutations.

q-bio.BM↗

arXiv2001

On the Extension Behavior of Helicogenic Polypeptides

The force laws governing the extension behavior of homopolypeptides are obtained from a phenomenological free energy capable of describing the helix-coil transition. Just above the melting temperature of the free chains, T*, the plot of force, f, vs. end-to-end distance, R, exhibits two plateaus associated with coexistence of helical and coil domains. The lower plateau is due to tension induced onset of helix-coil transition. The higher plateau corresponds to the melting of the helices by overextension. Just below T* the f-R plot exhibits only the upper plateau. The f-R plots, the helical fraction, the number of domains and their polydispersity are calculated for two models: In one the helical domains are viewed as rigid rods while in the second they are treated as worm like chains.

cond-mat.soft↗