Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

The piezo-phototronic effect has been promising as an effective means to improve the performance of two-dimensional (2D) semiconductor based optoelectronic devices. However, the current reported monolayer 2D semiconductors are not regarded as suitable for actual flexible piezotronic photodetectors due to their insufficient optical absorption and mechanical durability, although they possess strong piezoelectricity. In this work, we demonstrate that, unlike 2H-phase transition-metal dichalcogenides, γ-phase InSe with a hexagonal unit cell possesses broken inversion symmetry in all the layer numbers and has a strong second-harmonic generation effect. Moreover, driven by the piezo-phototronic effect, a flexible self-powered photodetector based on multilayer γ-InSe, which can work without any energy supply, is proposed. The device exhibited ultrahigh photon responsivity of 824 mA/W under light illuminations of 400 nm (0.368 mW/cm 2 ). Moreover, the responsivity and response speed of this photodetector were enhanced further by as much as 696% and 1010%, respectively, when a 0.62% uniaxial tensile strain was applied. Our devices exhibit high reliability and stability during a 6 month test time. These significant findings offer a promising pathway to construct high-performance flexible piezo-phototronic photodetectors based on multilayer 2D semiconductors.

Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e.g., to detect analytes in solution). To control and characterize peptide behavior on a graphene surface in solution is difficult. Here we successfully probed the molecular interactions between two peptides (cecropin P1 and MSI-78(C1)) and graphene in situ and in real-time using sum frequency generation (SFG) vibrational spectroscopy and molecular dynamics (MD) simulation. We demonstrated that the distribution of various planar (including aromatic (Phe, Trp, Tyr, and His)/amide (Asn and Gln)/Guanidine (Arg)) side-chains and charged hydrophilic (such as Lys) side-chains in a peptide sequence determines the orientation of the peptide adsorbed on a graphene surface. It was found that peptide interactions with graphene depend on the competition between both planar and hydrophilic residues in the peptide. Our results indicated that part of cecropin P1 stands up on graphene due to an unbalanced distribution of planar and hydrophilic residues, whereas MSI-78(C1) lies down on graphene due to an even distribution of Phe residues and hydrophilic residues. With such knowledge, we could rationally design peptides with desired residues to manipulate peptide-graphene interactions, which allows peptides to adopt optimized structure and exhibit excellent activity for nanobio-technological applications. This research again demonstrates the power to combine SFG vibrational spectroscopy and MD simulation in studying interfacial biological molecules.

Antimicrobial peptides, because of their unique structural and chemical properties, hold a promising future for the development of a new class of bacterial-resistant antibiotics, effective antimicrobial coatings, and high performance biosensors. To understand the structure/function relationship of surface-bound peptides as they relate to such applications, sum frequency generation (SFG) vibrational spectroscopy, coarse grained molecular dynamics simulations, and antimicrobial activity tests were used to characterize both surface peptide structural information and peptide activity. Results from MSI-78, an antimicrobial peptide, chemically immobilized via the N-(nMSI-78) or C-terminus (MSI-78n), demonstrate that the attachment site influences the structure and behavior of surface-bound peptides. Although both immobilized peptides adopt an α-helical structure in aqueous buffer, nMSI-78 stands up and MSI-78n lies down on the surface, as indicated by both SFG and MD simulations. Antimicrobial activity tests indicated that peptides that stand up interact with bacterial cells much quicker than peptides that lie down. We believe that this study provides fundamental insights into how to rationally engineer peptides and substrate surfaces to produce optimized abiotic/biotic interfaces for antimicrobial applications and beyond.

Immobilization on solid supports provides an effective way to improve enzyme stability and simplify downstream processing for biotechnological applications, which has been widely used in research and in applications. However, surface immobilization may disrupt enzyme structure due to interactions between the enzyme and the supporting substrate, leading to a loss of the enzyme catalytic efficiency and stability. Here, we use a model enzyme, nitroreductase (NfsB), to demonstrate that engineered variants with two strategically positioned surface-tethering sites exhibit improved enzyme stability when covalently immobilized onto a surface. Tethering sites were designed based on molecular dynamics (MD) simulations, and enzyme variants containing cysteinyl residues at these positions were expressed, purified, and immobilized on maleimide-terminated self-assembled monolayer (SAM) surfaces. Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy were used to deduce the NfsB enzyme orientations, which were found to be consistent with those predicted from the MD simulations. Thermal stability analyses demonstrated that NfsB variants immobilized through two tethering sites exhibited generally improved thermal stability compared with enzymes tethered at only one position. For example, NfsB enzyme chemically immobilized via positions 423 and 111 exhibits at least 60% stability increase compared to chemically immobilized NfsB mutant via a single site. This research develops a generally applicable and systematic approach using a combination of simulation and experimental methods to rationally select protein immobilization sites for the optimization of surface-immobilized enzyme activity and stability.

The interaction of proteins with surfaces is important in numerous applications in many fields-such as biotechnology, proteomics, sensors, and medicine--but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

Graphene-based biosensors have attracted considerable attention due to their advantages of label-free detection and high sensitivity. Many such biosensors utilize noncovalent van der Waals force to attach proteins onto graphene surface while preserving graphene's high conductivity. Maintaining the protein structure without denaturation/substantial conformational change and controlling proper protein orientation on the graphene surface are critical for biosensing applications of these biosensors fabricated with proteins on graphene. Based on the knowledge we obtained from our previous experimental study and computer modeling of amino acid residual level interactions between graphene and peptides, here we systemically redesigned an important protein for better conformational stability and desirable orientation on graphene. In this paper, immunoglobulin G (IgG) antibody-binding domain of protein G (protein GB1) was studied to demonstrate how we can preserve the protein native structure and control the protein orientation on graphene surface by redesigning protein mutants. Various experimental tools including sum frequency generation vibrational spectroscopy, attenuated total refection-Fourier transform infrared spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy were used to study the protein GB1 structure on graphene, supplemented by molecular dynamics simulations. By carefully designing the protein GB1 mutant, we can avoid strong unfavorable interactions between protein and graphene to preserve protein conformation and to enable the protein to adopt a preferred orientation. The methodology developed in this study is general and can be applied to study different proteins on graphene and beyond. With the knowledge obtained from this research, one could apply this method to optimize protein function on surfaces (e.g., to enhance biosensor sensitivity).

The lack of high-performance tactile sensors, especially for pressure/force, is a huge obstacle for the widespread application of intelligent robots. Current pressure sensors are often operated in the high range of pressure and normal direction, showing a little ability in the low range of pressure and three-axis direction simultaneously. Herein, a highly sensitive flexible tactile sensor with three-axis force sensing capacity is presented by combining microstructured polydimethylsiloxane (PDMS) arrays and a reduced graphene oxide (rGO) film. The deformation of microstructured rGO/PDMS results in a change in the contact area between the rGO film and electrode, leading to a high sensitivity of -1.71 kPa-1 in the low range pressure of 0-225 Pa with a fast response time of 6 ms at a large feature size of 100 μm. To realize three-axis sensing, a sensing unit was built up, which was composed of the adjacent four parts of patterns and electrodes underneath a bump. A mechanical model of the exerted spatial force was established to calculate each axis force component via the deformation of the rGO/PDMS pattern. The experimental results show that the current difference between the adjacent two parts has a strong relationship with the applied force. As a proof of concept, we have demonstrated a 3 × 3 array sensor for arbitrary force sensing. Our tactile sensor would be used in transmitting information from a gentle spatial force and would exhibit broad applications as e-skin in integrated robots.