Sensitive thermal transitions of nanoscale polymer samples using the bimetallic effect: Application to ultra-thin polythiophene

A sensitive nanocalorimetric technology based on microcantilever sensors is presented. The tech- nology, which combines very short response times with very small sample consumption, uses the bimetallic effect to detect thermal transitions. Specifically, abrupt variations in the Young’s modu- lus and the thermal expansion coefficient produced by temperature changes have been employed to detect thermodynamic transitions. The technology has been used to determine the glass transition of poly(3-thiophene methyl acetate), a soluble semiconducting polymer with different nanotechno- logical applications. The glass transition temperature determined using microcantilevers coated with ultra-thin films of mass = 10 − 13 gis5.2 ◦ C higher than that obtained using a conventional differential scanning calorimeter for bulk powder samples of mass = 5 × 10 − 3 g. Atomistic molecular dynamics simulations on models that represent the bulk powder and the ultra-thin films have been carried out to provide understanding and rationalization of this feature. Simulations indicate that the film-air in- terface plays a crucial role in films with very small thickness, affecting both the organization of the molecular chains and the response of the molecules against the temperature.Peer ReviewedPostprint (published version

IgG1-b12-HIV-gp120 interface in solution: a computational study

The use of broadly neutralizing antibodies against human immunodeficiency virus type 1 (HIV-1) has been shown to be a promising therapeutic modality in the prevention of HIV infection. Understanding the b12–gp120 binding mechanism under physiological conditions may assist the development of more broadly effective antibodies. In this work, the main conformations and interactions between the receptor-binding domain (RBD) of spike glycoprotein gp120 of HIV-1 and the IgG1-b12 mAb are studied. Accelerated molecular dynamics (aMD) and ab initio hybrid molecular dynamics have been combined to determine the most persistent interactions between the most populated conformations of the antibody–antigen complex under physiological conditions. The results show the most persistent receptor-binding mapping in the conformations of the antibody–antigen interface in solution. The binding-free-energy decomposition reveals a small enhancement in the contribution played by the CDR-H3 region to the b12–gp120 interface compared to the crystal structure.Peer ReviewedPostprint (author's final draft

Tethering of the IgG1 antibody to amorphous silica for immunosensor development: a molecular dynamics study

A key factor for improving the sensitivity and performance of immunosensors based on mechanical–plasmonic methods is the orientation of the antibody proteins immobilized on the inorganic surface. Although experimental techniques fail to determine surface phenomena at the molecular level, modern simulations open the possibility for improving our understanding of protein–surface interactions. In this work, replica exchange molecular dynamics (REMD) simulations have been used to model the IgG1 protein tethered onto the amorphous silica surface by considering a united-atom model and a relatively large system (2500 nm2 surface). Additional molecular dynamics (MD) simulations have been conducted to derive an atomistic model for the amorphous silica surface using the cristobalite crystal structure as a starting point and to examine the structure of the free IgG1 antibody in the solution for comparison when immobilized. Analyses of the trajectories obtained for the tethered IgG1, which was sampled considering 32 different temperatures, have been used to define the geometry of the protein with respect to the inorganic surface. The tilt angle of the protein with respect to the surface plane increases with temperature, the most populated values being 24, 66, and 87° at the lowest (250 K), room (298 K), and the highest (380 K) temperatures. This variation indicates that the importance of protein–surface interactions decreases with increasing temperature. The influence of the surface on the structure of the antibody is very significant in the constant region, which is directly involved in the tethering process, while it is relatively unimportant for the antigen-binding fragments, which are farthest from the surface. These results are expected to contribute to the development of improved mechanical–plasmonic sensor microarrays in the near future.Peer ReviewedPostprint (author's final draft

Sensitive thermal transitions of nanoscale polymer samples using the bimetallic effect: Application to ultra-thin polythiophene

A sensitive nanocalorimetric technology based on microcantilever sensors is presented. The tech- nology, which combines very short response times with very small sample consumption, uses the bimetallic effect to detect thermal transitions. Specifically, abrupt variations in the Young’s modu- lus and the thermal expansion coefficient produced by temperature changes have been employed to detect thermodynamic transitions. The technology has been used to determine the glass transition of poly(3-thiophene methyl acetate), a soluble semiconducting polymer with different nanotechno- logical applications. The glass transition temperature determined using microcantilevers coated with ultra-thin films of mass = 10 − 13 gis5.2 ◦ C higher than that obtained using a conventional differential scanning calorimeter for bulk powder samples of mass = 5 × 10 − 3 g. Atomistic molecular dynamics simulations on models that represent the bulk powder and the ultra-thin films have been carried out to provide understanding and rationalization of this feature. Simulations indicate that the film-air in- terface plays a crucial role in films with very small thickness, affecting both the organization of the molecular chains and the response of the molecules against the temperature.Peer Reviewe