The paper presents an ab initio method for calculating electronic structure, electronic transport, and forces acting on atoms in atomic-scale systems connected to semi-infinite electrodes with an applied voltage bias. The method is based on Density Functional Theory (DFT) as implemented in the SIESTA approach, which uses non-local norm-conserving pseudopotentials and linear combinations of finite-range numerical atomic orbitals. The method fully accounts for the atomistic structure of the entire system, treating both the contact and electrodes on an equal footing. The finite bias effect is considered using nonequilibrium Green's functions, and the method is applied to three systems: single-atom carbon wires connected to aluminum electrodes, single-atom gold wires, and large carbon nanotube systems with point defects. The method is validated by comparing results with earlier ab initio DFT calculations or experiments, highlighting differences between this method and existing schemes.The paper presents an ab initio method for calculating electronic structure, electronic transport, and forces acting on atoms in atomic-scale systems connected to semi-infinite electrodes with an applied voltage bias. The method is based on Density Functional Theory (DFT) as implemented in the SIESTA approach, which uses non-local norm-conserving pseudopotentials and linear combinations of finite-range numerical atomic orbitals. The method fully accounts for the atomistic structure of the entire system, treating both the contact and electrodes on an equal footing. The finite bias effect is considered using nonequilibrium Green's functions, and the method is applied to three systems: single-atom carbon wires connected to aluminum electrodes, single-atom gold wires, and large carbon nanotube systems with point defects. The method is validated by comparing results with earlier ab initio DFT calculations or experiments, highlighting differences between this method and existing schemes.