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Supported lipid bilayers (SLBs) are commonly used to investigate interactions between cell membranes and their environment. These model platforms can be formed on electrode surfaces and analyzed using electrochemical methods for bioapplications. Carbon nanotube porins (CNTPs) integrated with SLBs have emerged as promising artificial ion channel platforms. In this study, we present the integration and ion transport characterization of CNTPs in in vivo environments. We combine experimental and simulation data obtained from electrochemical analysis to analyze the membrane resistance of the equivalent circuits. Our results show that carrying CNTPs on a gold electrode results in high conductance for monovalent cations (K+ and Na+) and low conductance for divalent cations (Ca2+).

Ultra reliable and low latency communications (URLLC) is a new service category in 5G to accommodate emerging services and applications having stringent latency and reliability requirements. In order to support URLLC, there should be both evolutionary and revolutionary changes in the air interface named 5G new radio (NR). In this article, we provide an up-to-date overview of URLLC with an emphasis on the physical layer challenges and solutions in 5G NR downlink. We highlight key requirements of URLLC and then elaborate the physical layer issues and enabling technologies including packet and frame structure, scheduling schemes, and reliability improvement techniques, which have been discussed in the 3GPP Release 15 standardization., Comment: Copyright 2018 IEEE. Permission from IEEE must be obtained for all other uses,in any current or future media,including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works

Ultra reliable and low latency communication (URLLC) is a newly introduced service category in 5G to support delay-sensitive applications. In order to support this new service category, 3rd Generation Partnership Project (3GPP) sets an aggressive requirement that a packet should be delivered with 10^-5 packet error rate within 1 ms transmission period. Since the current wireless transmission scheme designed to maximize the coding gain by transmitting capacity achieving long codeblock is not relevant for this purpose, a new transmission scheme to support URLLC is required. In this paper, we propose a new approach to support the short packet transmission, called sparse vector coding (SVC). Key idea behind the proposed SVC technique is to transmit the information after the sparse vector transformation. By mapping the information into the position of nonzero elements and then transmitting it after the random spreading, we obtain an underdetermined sparse system for which the principle of compressed sensing can be applied. From the numerical evaluations and performance analysis, we demonstrate that the proposed SVC technique is very effective in URLLC transmission and outperforms the 4G LTE and LTE-Advanced scheme., Comment: To appear in IEEE Transactions on Wireless Communications. Copyright 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses

Nanotechnology has held great promise for revolutionizing biology. The biological behavior of nanomaterials depends primarily on how they interface to biomolecules and their surroundings. Unfortunately, interface issues like non-specific adsorption are still the biggest obstacles to the success of nanobiotechnology and nanomedicine, and have held back widespread practical use of nanotechnology in biology. Not only does the biological interface of nanoparticles (NPs) need to be understood and controlled, but also NPs must be treated as biological entities rather than inorganic ones. Furthermore, one can adopt an engineering perspective of the NP–biological interface, realizing that it has unique, exploitable properties., National Institutes of Health (U.S.) (R21 EB008156-01), National Science Foundation (U.S.) (DMR 0906838)

Multiclass problems are often decomposed into multiple binary problems that are solved by individual binary classifiers whose results are integrated into a final answer. Various methods, including all-pairs (APs), one-versus-all (OVA), and error correcting output code (ECOC), have been studied, to decompose multiclass problems into binary problems. However, little study has been made to optimally aggregate binary problems to determine a final answer to the multiclass problem. In this paper we present a convex optimization method for an optimal aggregation of binary classifiers to estimate class membership probabilities in multiclass problems. We model the class membership probability as a softmax function which takes a conic combination of discrepancies induced by individual binary classifiers, as an input. With this model, we formulate the regularized maximum likelihood estimation as a convex optimization problem, which is solved by the primal-dual interior point method. Connections of our method to large margin classifiers are presented, showing that the large margin formulation can be considered as a limiting case of our convex formulation. Numerical experiments on synthetic and real-world data sets demonstrate that our method outperforms existing aggregation methods as well as direct methods, in terms of the classification accuracy and the quality of class membership probability estimates., Comment: Appeared in Proceedings of the 2014 SIAM International Conference on Data Mining (SDM 2014)

The effective hydrodynamic size and free mobility of particles of varying aspect ratio were evaluated by Ferguson analysis of gel electrophoresis. The ligand layer thickness was estimated from the difference between the effective size and the size of the metal core from TEM imaging. The zeta potential of the particles was calculated from the Ferguson analysis result by applying conventional electrophoresis theories for spheres and cylinders. The results show that Henry’s solution for spherical particles can be used to obtain the zeta potential of cylindrical particles without requiring the use of TEM for size analysis., National Science Foundation (U.S.) (DMR 0906838)

Gold nanoparticle (AuNP)−DNA conjugates can enhance in vitro translation of a protein. Enhancement occurs via a combination of nonspecific adsorption of translation-related molecules and the ribosome to the AuNP−DNA and specific binding to the mRNA of interest. AuNP−DNA conjugates enhanced protein production of fluorescent proteins (mCherry, eGFP) in retic lysate mixes by 65−100%. Gel electrophoresis was used to probe nonspecific adsorption of the AuNP−DNA conjugates to the translation machinery. It was determined that nonspecific adsorption is critical for enhancement, and if it was eliminated, expression enhancement did not occur. The interaction of the mRNA with the DNA on the AuNP surface influenced the amount of enhancement and was probed by expression in the presence of RNase H. These results suggest that higher translation enhancement occurs when the DNA on the AuNP forms an incomplete duplex with the mRNA. Tuning the balance between nonspecific adsorption and specific binding of the AuNP−DNA conjugates could result in the translation enhancement of a specific gene in a mixture., National Institute of Biomedical Imaging and Bioengineering (U.S.) (R21 EB008156-01)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009., Includes bibliographical references., Nano-science has exploited the hybridization and de-hybridization phenomena of DNA which are one of its fundamental functions. In particular, conjugates of gold nanoparticles and DNA (Au NP-DNA) have been extensively explored for their potential in biological applications such as DNA delivery for gene therapy and disease detection. However, DNA strands are known to adsorb onto the Au NP surface, which can severely limit the hybridization ability of Au NP-DNA conjugates. Therefore, methods of chemical modification of Au NP surfaces and evaluating DNA conformation via Ferguson analysis of gel electrophoresis are proposed in the thesis. Conjugates of DNA with Au NP of different sizes and coverages are evaluated with Ferguson analysis to characterize important parameters such as hydrodynamic size and zeta-potential. Surface modified Au NP exhibits enhanced stability and hybridization specificity in the system, which infers the effectiveness of those methods towards biological systems where non-specific adsorption is problematic. To confirm the validity of the concept, Au NP-antisense DNA experiments for gene silencing are performed in the work. Antisense DNA is designed to inhibit ribosomal activity on mRNAs and cooperatively works with Au NPs to enhance physical blocking mechanisms. However, the result shows that Au NP-DNA conjugates can enhance in vitro gene expression depending on DNA sequence and coverage of the conjugates. Suggestions are made for further investigation on proof and improvement of the translation enhancer concept., by Sunho Park., Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009., Includes bibliographical references., Nano-science has exploited the hybridization and de-hybridization phenomena of DNA which are one of its fundamental functions. In particular, conjugates of gold nanoparticles and DNA (Au NP-DNA) have been extensively explored for their potential in biological applications such as DNA delivery for gene therapy and disease detection. However, DNA strands are known to adsorb onto the Au NP surface, which can severely limit the hybridization ability of Au NP-DNA conjugates. Therefore, methods of chemical modification of Au NP surfaces and evaluating DNA conformation via Ferguson analysis of gel electrophoresis are proposed in the thesis. Conjugates of DNA with Au NP of different sizes and coverages are evaluated with Ferguson analysis to characterize important parameters such as hydrodynamic size and zeta-potential. Surface modified Au NP exhibits enhanced stability and hybridization specificity in the system, which infers the effectiveness of those methods towards biological systems where non-specific adsorption is problematic. To confirm the validity of the concept, Au NP-antisense DNA experiments for gene silencing are performed in the work. Antisense DNA is designed to inhibit ribosomal activity on mRNAs and cooperatively works with Au NPs to enhance physical blocking mechanisms. However, the result shows that Au NP-DNA conjugates can enhance in vitro gene expression depending on DNA sequence and coverage of the conjugates. Suggestions are made for further investigation on proof and improvement of the translation enhancer concept., by Sunho Park., Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2004., Includes bibliographical references (leaves 77-82)., Metal nanoparticles can be used as antennae covalently linked to biomolecules. External alternating magnetic field can turn on and off the biological activity of the molecules due to induction heating from the particles that changes the temperature around the molecules. Here an experimental scheme towards direct temperature probing is proposed to predict the behavior of the antenna. Oligonucleotides modified with photosensitive molecules are conjugated with gold nanoparticles and report the temperature at their positions within some nanometers' distance from the particles. However, oligos have a known tendency to stick to gold surfaces. To locate the probes at desired position, 6-mercapto-1-hexanol (MCH) is used to reduce oligonucleotides' adsorption to the surface of gold. The experimental result shows that oligos on particle's surface can be stretched radially without any reduction of coverage ratio. Optimal MCH concentration and reaction time highly depend on the concentration of MCH and the conjugates as well as reaction time and the size of the molecules., by Sunho Park., S.M.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2004., Includes bibliographical references (leaves 77-82)., Metal nanoparticles can be used as antennae covalently linked to biomolecules. External alternating magnetic field can turn on and off the biological activity of the molecules due to induction heating from the particles that changes the temperature around the molecules. Here an experimental scheme towards direct temperature probing is proposed to predict the behavior of the antenna. Oligonucleotides modified with photosensitive molecules are conjugated with gold nanoparticles and report the temperature at their positions within some nanometers' distance from the particles. However, oligos have a known tendency to stick to gold surfaces. To locate the probes at desired position, 6-mercapto-1-hexanol (MCH) is used to reduce oligonucleotides' adsorption to the surface of gold. The experimental result shows that oligos on particle's surface can be stretched radially without any reduction of coverage ratio. Optimal MCH concentration and reaction time highly depend on the concentration of MCH and the conjugates as well as reaction time and the size of the molecules., by Sunho Park., S.M.