I am happy to announce the publication of a book "Simulations in Nanobiotechnology", which was contributed from researchers (including iMechanicians) who have expertise in the area of nanobiotechnology. The book is aimed at presenting the current state-of-arts in computational simulations of biological objects such as proteins as well as nanomaterials such as graphene, and also bio-nano-hybrid system such as nanopore-biomolecule interactions. This book provides the insight into the simulation-based characterization in nanobiotechnology.

Nanomechanical Actuation Driven by Light-Induced DNA Fuel

Kilho Eom, Huihun Jung, Gyudo Lee, Jinsung Park, Kihwan Nam, Sang Woo Lee, Dae Sung Yoon, Jaemoon Yang, and Taeyun Kwon

Abstract

Single-Molecule Recognition of Biomolecular Interaction via Kelvin Probe Force Microscopy  

Jinsung Park, Jaemoon Yang, Gyudo Lee, Chang Young Lee, Sungsoo Na, Sang Woo Lee, Seungjoo Haam, Yong-Min Huh, Dae Sung Yoon, Kilho Eom*, Taeyun Kwon*

Mechanical Characterization of Amyloid Fibrils Using Coarse-Grained Normal Mode Analysis

Gwonchan Yoon, Jinhak Kwak, Jae In Kim, Sungsoo Na, and Kilho Eom

Abstract

Finite Size Effect on Nanomechanical Mass Detection: Role of Surface Elasticity

Mai Duc Dai, Chang-Wan Kim, and Kilho Eom 

Abstract

Nanomechanical Resonators and Their Applications in Biological/Chemical Detection: Nanomechanics Principles

Kilho Eom, Harold S. Park, Dae Sung Yoon, Taeyun Kwon 

Abstract

Abstract

Dear. Collegue

We have recently suggested the potential of resonant microcantilever for quantitative study on the kinetics of biomolecular interactions such as protein-protein interaction and DNA hybridization. We have employed the Langmuir kinetic model for describing the molecular interactions on the surface, which leads to change of overall mass of cantilever responsible for resonant frequency shift. Such Langmuir kinetic model dictates the in situ resonant frequency shift due to biomolecular interaction in liquid. This indicates that resonant cantilever is able to provide the information of biochemical reaction. This work was published in Applied Physics Letters in Oct 31, 2008.

We consider the mesoscopic model of protein materials composed of protein crystals with given space group for understanding the mechanical properties of protein materials with respect to their structures. This preprint was accepted for publication at Journal of Computational Chemistry.

The preprint provides the summary and/or review of current state-of-art in coarse-grained modeling of protein structures for normal mode analysis. This review summarizes the quasiharmonic analysis, Go model, elastic network model, and recently suggested coarse-grained models for protein structures.

Abstract 

We made a simple model for understanding the dynamic behavior of nanomechanical resonator in response to biomolecular interactions. Specifically, in our model, we considered the nanomechanical resonator, on whose surface the biomolecules (dsDNA) are adsorbed, such that Hamiltonian of the system consists of elastic bending energy of nanomechanical resonator and potential energy for biomolecular interaction (i.e. DNA-DNA interaction). It was shown that DNA-DNA interaction plays a role on the resonant frequency shift for nano-scale resonators. This work was accepted for publications at Physical Review B.

Dynamical Response of Nanomechanical Resonators to Biomolecular Interactions

We have recently reported the label-free detection of HCV (Hepatitis C Virus) helicase by using a resonating microcantilever whose surface is functionalized by RNA aptamers as receptor molecules. This work was accepted for publication at Biosensors & Bioelectronics.

Abstract

We have recently reported the piezoelectric thick film microcantilever, which enables the in-situ real-time detection of the protein related to disease (e.g. C reactive protein) in liquid environment. This work was published at APL (click here).

"In-situ real-time monitoring of biomolecular interactions based on resonating microcantilevers immersed in a viscous fluid"

We recently reported the mass sensing by using resonating microcantilevers. The characterization of mass-sensing and its related sensitivity was suggested on the basis of elasticity theory. This work was published online at Sensors and Actuators A (click here).

Recently, I reported the model reduction method for large proteins for understanding large protein dynamics based on low-frequency normal modes. This work was pubslihed at Journal of Computational Chemistry (click here).

Coarse-Graining of protein structures for the normal mode studies

Abstracts 

There has been a lot of attention on the study of mechanics of proteins and/or single molecules. Such study was typically implemented by using classical molecular dynamics (MD) simulation. In spite of ability to describe the dynamics of biological macromolecules (e.g. proteins), MD simulation exhibits the computational restriction in the spatial and temporal scale. In order to overcome such computational limitation, the coarse-grained model has recently been taken into account. In this review, I would take a look at a couple of coarse-grained models of protein molecules.

Microcantilevers have taken much attention as devices for label-free detection of molecules and/or their conformations in solutions and air. Recently, microcantilevers have allowed the nanomechanical mass detection of thin film [1-3], small molecules [4, 5], and biological components such as viruses [6] and vesicles [7] in the order of a pico-gram to a zepto-gram. The great potential of microcantilevers is the sensitive, reliable, fast label-free detection of proteins and/or protein conformations. Specifically, microcantilevers are capable of label-free detection of marker proteins related to diseases, even at a low concentration in solution [8-17]. Microcantilevers, operated in a viscous fluid, have also enabled the real-time monitoring of protein-protein interactions [8, 12-15]. Furthermore, microcantilevers are able to recognize the specific protein conformations [18] and/or reversible conformation changes of proteins/polymers [19, 20].

The conference "micro-TAS" may be interesting to researchers in engineering and science, especially involving Bio-MEMS/NEMS, biophysics, and biochemistry. See details of this conference.